pax_global_header 0000666 0000000 0000000 00000000064 14036164772 0014524 g ustar 00root root 0000000 0000000 52 comment=1d0bfe30d42c1d970f003c09cbf2b43ce9d3871e
kalign-3.3.1/ 0000775 0000000 0000000 00000000000 14036164772 0012775 5 ustar 00root root 0000000 0000000 kalign-3.3.1/.github/ 0000775 0000000 0000000 00000000000 14036164772 0014335 5 ustar 00root root 0000000 0000000 kalign-3.3.1/.github/workflows/ 0000775 0000000 0000000 00000000000 14036164772 0016372 5 ustar 00root root 0000000 0000000 kalign-3.3.1/.github/workflows/ccpp.yml 0000664 0000000 0000000 00000001646 14036164772 0020051 0 ustar 00root root 0000000 0000000 name: C/C++ CI
on: [push]
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v1
- name: autogen
run: ./autogen.sh
- name: configure
run: ./configure --prefix $HOME
- name: make
run: make
- name: make check
run: make check
- name: make distcheck
run: make distcheck
- name: make install
run: make install
- name: kalign version
run: ~/bin/kalign -v
build-mac:
runs-on: macos-latest
steps:
- uses: actions/checkout@v1
- name: install build tools
run: brew install automake
- name: autogen
run: ./autogen.sh
- name: configure
run: ./configure --prefix $HOME
- name: make
run: make
- name: make check
run: make check
- name: make distcheck
run: make distcheck
- name: make install
run: make install
- name: kalign version
run: kalign -v kalign-3.3.1/.github/workflows/codeql-analysis.yml 0000664 0000000 0000000 00000004445 14036164772 0022214 0 ustar 00root root 0000000 0000000 name: "CodeQL"
on:
push:
branches: [master]
pull_request:
# The branches below must be a subset of the branches above
branches: [master]
schedule:
- cron: '0 2 * * 4'
jobs:
analyze:
name: Analyze
runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
# Override automatic language detection by changing the below list
# Supported options are ['csharp', 'cpp', 'go', 'java', 'javascript', 'python']
language: ['cpp']
# Learn more...
# https://docs.github.com/en/github/finding-security-vulnerabilities-and-errors-in-your-code/configuring-code-scanning#overriding-automatic-language-detection
steps:
- name: Checkout repository
uses: actions/checkout@v2
with:
# We must fetch at least the immediate parents so that if this is
# a pull request then we can checkout the head.
fetch-depth: 2
# If this run was triggered by a pull request event, then checkout
# the head of the pull request instead of the merge commit.
- run: git checkout HEAD^2
if: ${{ github.event_name == 'pull_request' }}
# Initializes the CodeQL tools for scanning.
- name: Initialize CodeQL
uses: github/codeql-action/init@v1
with:
languages: ${{ matrix.language }}
# If you wish to specify custom queries, you can do so here or in a config file.
# By default, queries listed here will override any specified in a config file.
# Prefix the list here with "+" to use these queries and those in the config file.
# queries: ./path/to/local/query, your-org/your-repo/queries@main
# Autobuild attempts to build any compiled languages (C/C++, C#, or Java).
# If this step fails, then you should remove it and run the build manually (see below)
- name: Autobuild
uses: github/codeql-action/autobuild@v1
# âšī¸ Command-line programs to run using the OS shell.
# đ https://git.io/JvXDl
# âī¸ If the Autobuild fails above, remove it and uncomment the following three lines
# and modify them (or add more) to build your code if your project
# uses a compiled language
#- run: |
# make bootstrap
# make release
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v1
kalign-3.3.1/.gitignore 0000664 0000000 0000000 00000000400 14036164772 0014757 0 ustar 00root root 0000000 0000000 GPATH
GRTAGS
GTAGS
*.o
Makefile
Makefile.in
src/GPATH
src/GRTAGS
src/GTAGS
src/build_ihmm
src/build_model
src/libihmm.a
src/plot_model
src/sim_seq
INSTALL
aclocal.m4
autom4te.cache/
compile
configure
configure.scan
depcomp
install-sh
missing
test-driver
kalign-3.3.1/.gitmodules 0000664 0000000 0000000 00000000000 14036164772 0015140 0 ustar 00root root 0000000 0000000 kalign-3.3.1/AUTHORS 0000664 0000000 0000000 00000000015 14036164772 0014041 0 ustar 00root root 0000000 0000000 Timo Lassmann kalign-3.3.1/COPYING 0000664 0000000 0000000 00000104513 14036164772 0014034 0 ustar 00root root 0000000 0000000 GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc.
Everyone is permitted to copy and distribute verbatim copies
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Also add information on how to contact you by electronic and paper mail.
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Public License instead of this License. But first, please read
.
kalign-3.3.1/ChangeLog 0000664 0000000 0000000 00000007361 14036164772 0014556 0 ustar 00root root 0000000 0000000 2021-04-16 Timo Lassmann
* version 3.3.1 - Bug Fix
The previous version kalign checked the top 50 sequences in inputs to determine
whether the sequences are aligned or not. If the first 50 sequences are not aligned,
but following sequences contain gaps (or other characters!) kalign can crash. In this
version (3.3.1) kalign checks all sequences, thereby avoiding this issue.
To alert users to the situation described above and to warn users about the presence of
odd characters, kalign now produces a warning message like this:
[Date Time] : LOG : Start io tests.
[Date Time] : LOG : reading: dev/data/a2m.good.1
[Date Time] : LOG : Detected protein sequences.
[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 505)
[Date Time] : WARNING : The input sequences contain gap characters: (rwalign.c line 506)
[Date Time] : WARNING : "-" : 36 found (rwalign.c line 510)
[Date Time] : WARNING : BUT the sequences do not seem to be aligned! (rwalign.c line 514)
[Date Time] : WARNING : (rwalign.c line 515)
[Date Time] : WARNING : Kalign will remove the gap characters and (rwalign.c line 516)
[Date Time] : WARNING : align the sequences. (rwalign.c line 517)
[Date Time] : WARNING : -------------------------------------------- (rwalign.c line 518)
2020-11-06 Timo Lassmann
* version 3.3 - Threading and more
- Kalign now runs pairwise distance estimation, guide tree building and alignments in parallel.
- Memory optimisations.
- Optimised bi-sectional K-means algorithm.
- added -clean option to check for sequences with identical names but different sequences.
- fixed minor bug in alignment I/O module
2020-09-24 Timo Lassmann
* version 3.2.7 - Development version
- dynamic programming in now more modular.
- fixed rare bug in alignment input / output
- added gap parameters (--gpo, --gpe, --tgpe)
- for protein alignment I now use the CorBLOSUM66_13plus matrix from:
Hess M, Keul F, Goesele M, Hamacher K.
Addressing inaccuracies in BLOSUM computation improves homology search performance.
BMC bioinformatics. 2016 Dec 1;17(1):189.
with the empirically derived gap penalties.
2020-04-22 Timo Lassmann
* version 3.2.5
- Bug fix: when given long output named the first lines in msf
output could be truncated.
2020-04-01 Timo Lassmann
* version 3.2.4
- Fixed issue relating to stdin input on clusters.
- Added more sanity checks
2020-03-16 Timo Lassmann
* version 3.2.3
- replaced timing code with code from the easel lib.
2020-02-23 Timo Lassmann
* version 3.2.2
- Fixed minor bug in rwaln test routine. It assumed that input alignments
were correctly formatted (which was not true for one test case). The
kalign executable was never affected by this.
- Added a script to test a few alignments.
2020-02-22 Timo lassmann
* version 3.2.1
minor bug fix removed "-lrt" required for old glibc versions and replaced
with a search in configure.ac: AC_SEARCH_LIBS([clock_gettime],[rt])
2020-02-15 Timo Lassmann
* version 3.2.0
Added support for reading sequences from standard input:
cat file.fasta | kalign -f fasta | ....
Added support for combining multiple input files into one alignment:
kalign sequencesA.fa sequencesB.fa > msa.fa
Also works in combination:
cat file.fasta | kalign sequencesA.fa sequencesB.fa > msa.fa
Minor:
- added m4 macros to enable / disable compiler flags
- added m4 macro for valgrind. Now there is a make target
called check-valgrind that run all tests through valgrind.
kalign-3.3.1/INSTALL 0000664 0000000 0000000 00000036614 14036164772 0014040 0 ustar 00root root 0000000 0000000 Installation Instructions
*************************
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kalign-3.3.1/Makefile.am 0000664 0000000 0000000 00000000555 14036164772 0015036 0 ustar 00root root 0000000 0000000 EXTRA_DIST = version.sh autogen.sh VERSION
ACLOCAL_AMFLAGS = -I m4
# Build the library in the hand subdirectory first
LIB_TLDEVELDIR = @LIB_TLDEVELDIR@
# top_builddir = @top_builddir@
SUBDIRS = src dev
count:
line=$$(find . \( -name "*.[c,h]" -o -name "*.am" -o -name "*.org" -o -name "*.sh" \) -type f -print0 | xargs -0 wc -l | grep total); echo $$line
kalign-3.3.1/NEWS 0000664 0000000 0000000 00000000000 14036164772 0013462 0 ustar 00root root 0000000 0000000 kalign-3.3.1/README 0000664 0000000 0000000 00000005315 14036164772 0013661 0 ustar 00root root 0000000 0000000 -----------------------------------------------------------------------
Kalign - a multiple sequence alignment program
Copyright 2006, 2019, 2020, 2021 Timo Lassmann
This file is part of kalign.
Kalign is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see .
-----------------------------------------------------------------------
Kalign is a fast multiple sequence alignment program for biological sequences.
1) Installation
1.1) Release Tarball
Download tarball from [releases](https://github.com/TimoLassmann/kalign/releases). Then:
tar -zxvf kalign-.tar.gz
cd kalign-
./autogen.sh
./configure
make
make check
make install
1.2) Homebrew
brew install brewsci/bio/kalign
1.3) Developer version
git clone https://github.com/TimoLassmann/kalign.git
cd kalign
./autogen.sh
./configure
make
make check
make install
1.4) on macOS, install [brew](https://brew.sh/) then:
brew install libtool
brew install automake
git clone https://github.com/TimoLassmann/kalign.git
cd kalign
./autogen.sh
./configure
make
make check
make install
2) Usage
Usage: kalign -i -o
Options:
--format : Output format. [Fasta]
--reformat : Reformat existing alignment. [NA]
--version : Print version and exit
Kalign expects the input to be a set of unaligned sequences in fasta format or aligned sequences in aligned fasta, MSF or clustal format. Kalign automatically detects whether the input sequences are protein, RNA or DNA.
Since version 3.2.0 kalign supports passing sequence in via stdin and support alignment of sequences from multiple files.
3) Examples
Passing sequences via stdin:
cat input.fa | kalign -f fasta > out.afa
Combining multiple input files:
kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
Align sequences and output the alignment in MSF format:
kalign -i BB11001.tfa -f msf -o out.msf
Align sequences and output the alignment in clustal format:
kalign -i BB11001.tfa -f clu -o out.clu
Re-align sequences in an existing alignment:
kalign -i BB11001.msf -o out.afa
Reformat existing alignment:
kalign -i BB11001.msf -r afa -o out.afa
kalign-3.3.1/README.md 0000664 0000000 0000000 00000006677 14036164772 0014274 0 ustar 00root root 0000000 0000000 

# Kalign
Kalign is a fast multiple sequence alignment program for biological sequences.
# Installation
## Release Tarball
Download tarball from [releases](https://github.com/TimoLassmann/kalign/releases). Then:
``` bash
tar -zxvf kalign-.tar.gz
cd kalign-
./autogen.sh
./configure
make
make check
make install
```
## Homebrew
``` bash
brew install brewsci/bio/kalign
```
## Developer version
``` bash
git clone https://github.com/TimoLassmann/kalign.git
cd kalign
./autogen.sh
./configure
make
make check
make install
```
on macOS, install [brew](https://brew.sh/) then:
``` bash
brew install libtool
brew install automake
git clone https://github.com/TimoLassmann/kalign.git
cd kalign
./autogen.sh
./configure
make
make check
make install
```
# Usage
``` bash
Usage: kalign -i -o
Options:
--format : Output format. [Fasta]
--reformat : Reformat existing alignment. [NA]
--version : Print version and exit
```
Kalign expects the input to be a set of unaligned sequences in fasta format or aligned sequences in aligned fasta, MSF or clustal format. Kalign automatically detects whether the input sequences are protein, RNA or DNA.
Since version 3.2.0 kalign supports passing sequence in via stdin and support alignment of sequences from multiple files.
# Examples
Passing sequences via stdin:
```
cat input.fa | kalign -f fasta > out.afa
```
Combining multiple input files:
```
kalign seqsA.fa seqsB.fa seqsC.fa -f fasta > combined.afa
```
Align sequences and output the alignment in MSF format:
```
kalign -i BB11001.tfa -f msf -o out.msf
```
Align sequences and output the alignment in clustal format:
```
kalign -i BB11001.tfa -f clu -o out.clu
```
Re-align sequences in an existing alignment:
```
kalign -i BB11001.msf -o out.afa
```
Reformat existing alignment:
```
kalign -i BB11001.msf -r afa -o out.afa
```
# Benchmark results
Here are some benchmark results. The code to reproduce these figures can be found at [here](scripts/benchmark.org).
## Balibase

## Bralibase

## Homfam

## Quantest2

# Please cite:
1. Lassmann, Timo. _Kalign 3: multiple sequence alignment of large data sets._ **Bioinformatics** (2019). [pdf](https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz795/30314127/btz795.pdf)
# Other papers:
1. Lassmann, Timo, Oliver Frings, and Erik LL Sonnhammer. _Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features._ **Nucleic acids research** 37.3 (2008): 858-865. [Pubmed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2647288/)
2. Lassmann, Timo, and Erik LL Sonnhammer. _Kalign: an accurate and fast multiple sequence alignment algorithm._ **BMC bioinformatics** 6.1 (2005): 298. [Pubmed](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1325270/)
kalign-3.3.1/VERSION 0000664 0000000 0000000 00000000005 14036164772 0014040 0 ustar 00root root 0000000 0000000 3.2.0 kalign-3.3.1/autogen.sh 0000775 0000000 0000000 00000002321 14036164772 0014774 0 ustar 00root root 0000000 0000000 #!/usr/bin/env sh
exists()
{
command -v "$1" >/dev/null 2>&1
}
if ! exists libtoolize; then
if ! exists glibtoolize; then
echo 'libtool/glibtool not found!'
echo 'to install using homebrew:'
echo 'brew install libtool'
exit 1
fi
fi
if ! exists aclocal; then
echo 'aclocal not found!'
echo 'to install using homebrew:'
echo 'brew install automake'
exit 1
fi
if ! exists autoheader; then
echo 'autoheader not found!'
echo 'to install using homebrew:'
echo 'brew install automake'
exit 1
fi
if ! exists automake; then
echo 'automake not found!'
echo 'to install using homebrew:'
echo 'brew install automake'
exit 1
fi
if ! exists autoconf; then
echo 'autoconf not found!'
echo 'to install using homebrew:'
echo 'brew install automake'
exit 1
fi
test -n "$srcdir" || srcdir=`dirname "$0"`
test -n "$srcdir" || srcdir=.
cd "$srcdir"
case `uname` in Darwin*) glibtoolize --force --copy ;;
*) libtoolize --force --copy ;;
esac
aclocal -I m4 $AL_OPTS
autoheader $AH_OPTS
automake --add-missing --copy --gnu $AM_OPTS
autoconf $AC_OPTS
echo
echo "Now run '$srcdir/configure' and 'make' to compile."
echo
kalign-3.3.1/configure.ac 0000664 0000000 0000000 00000010321 14036164772 0015260 0 ustar 00root root 0000000 0000000 AC_INIT(kalign, 3.3.1)
#AC_CONFIG_AUX_DIR([.])
AC_USE_SYSTEM_EXTENSIONS
AM_INIT_AUTOMAKE
# Checks for programs.
AC_PROG_AWK
AC_PROG_CC
AC_PROG_CXX
AC_PROG_INSTALL
AC_PROG_RANLIB
AM_SILENT_RULES([no])
LT_INIT
AC_CONFIG_MACRO_DIR([m4])
m4_include([m4/ax_ext.m4])
m4_include([m4/ax_valgrind_check.m4])
m4_include([m4/ax_check_compile_flag.m4])
m4_include([m4/ax_set_compile_flags.m4])
AX_EXT
AX_ENABLE_DEBUG
AC_ARG_ENABLE(openmp, [AC_HELP_STRING([--enable-openmp],[use OpenMP directives for parallelism])], enable_openmp=$enableval, enable_openmp=no)
if test "$enable_openmp" = "yes"; then
AC_DEFINE(HAVE_OPENMP,1,[Define to enable OpenMP])
AX_OPENMP([], [AC_MSG_ERROR([don't know how to enable OpenMP])])
fi
AC_SUBST(SIMD_FLAGS)
AC_ARG_WITH([openmp],
AS_HELP_STRING([--without-openmp], [Do not use OpenMP]))
AS_IF([test "x$with_openmp" = "xno"],
[],
[AX_OPENMP(
AC_DEFINE([HAVE_OPENMP],[1],[Defined if OpenMP should and can be used])
)]
)
AC_SUBST(OPENMP_CFLAGS)
# according to http://beagle-lib.googlecode.com/svn-history/r824/trunk/configure.ac:
# "OpenMP checker only defines for C when compiling both C and C++"
OPENMP_CXXFLAGS=$OPENMP_CFLAGS
AC_SUBST(OPENMP_CXXFLAGS)
# test for working C11 _Generic support
AN_IDENTIFIER([_Generic], [AC_C__GENERIC])
AC_DEFUN([AC_C__GENERIC],
[AC_CACHE_CHECK([for _Generic], ac_cv_c__Generic,
[AC_COMPILE_IFELSE(
[AC_LANG_SOURCE(
[[int
main (int argc, char **argv)
{
int a = _Generic (argc, int: argc = 1);
int *b = &_Generic (argc, default: argc);
char ***c = _Generic (argv, int: argc, default: argv ? &argv : 0);
_Generic (1 ? 0 : b, int: a, default: b) = &argc;
_Generic (a = 1, default: a) = 3;
return a + !b + !c;
}
]])],
[ac_cv_c__Generic=yes],
[ac_cv_c__Generic=no])])
if test $ac_cv_c__Generic = no; then
echo "-------------------------------------------"
echo " Unable to compile C11 code on this system!"
echo "-------------------------------------------"
echo ""
echo "Install a new(er) version of GCC (e.g. GCC 4.9+)"
echo "or clang!"
echo ""
AC_MSG_ERROR([ERROR: C compiler too old!])
AC_MSG_ERROR([We could not compile a simple C11 example. Install a new(er) compiler version (e.g. GCC 4.9).])
fi
])# AC_C__GENERIC
# Check for C11 _Generic support
AC_C__GENERIC
AC_CHECK_LIB([m], [sqrt])
AC_CHECK_LIB([pthread], [main])
AC_SEARCH_LIBS([clock_gettime],[rt posix])
# Checks for header files.
AC_CHECK_HEADERS([math.h float.h stdlib.h unistd.h])
AC_CHECK_HEADERS([sys/time.h])
AC_CHECK_HEADERS([mach/mach.h])
AC_CHECK_HEADERS([limits.h])
AC_C_INLINE
AC_TYPE_SIZE_T
AC_TYPE_SSIZE_T
AC_TYPE_INT8_T
AC_TYPE_INT32_T
AC_TYPE_INT16_T
AC_TYPE_INT64_T
AC_TYPE_UINT8_T
AC_TYPE_UINT16_T
AC_TYPE_UINT32_T
AC_TYPE_UINT64_T
# Checks for library functions.
AC_FUNC_MALLOC
AC_FUNC_REALLOC
AC_FUNC_STRNLEN
AC_FUNC_ERROR_AT_LINE
AC_CHECK_FUNCS([gettimeofday pow realpath sqrt strstr memset])
AC_CHECK_FUNCS([clock_gettime])
AC_CHECK_FUNCS([gethrtime])
AC_CHECK_FUNCS([gettimeofday])
AC_CHECK_FUNCS([localtime_r])
AC_CHECK_FUNCS([strcspn])
AC_CANONICAL_HOST
case $host_os in
darwin* )
DEAD_STRIP="-Wl,-dead_strip"
;;
*)
DEAD_STRIP="-Wl,--gc-sections -Wl,--as-needed"
;;
esac
AC_SUBST(DEAD_STRIP)
AX_VALGRIND_DFLT([memcheck], [on])
AX_VALGRIND_CHECK
AC_CONFIG_FILES([Makefile
src/Makefile dev/Makefile])
AC_CONFIG_HEADER([src/config.h])
AC_OUTPUT
AC_MSG_NOTICE([---------------------------------------------------------])
AC_MSG_NOTICE([Configuration complete - $PACKAGE_NAME-$PACKAGE_VERSION])
AC_MSG_NOTICE([])
AC_MSG_NOTICE([General Information:])
AC_MSG_NOTICE([ Version: $VERSION])
AC_MSG_NOTICE([ Configured on: $DATE])
AC_MSG_NOTICE([ Configured by: $USER])
AC_MSG_NOTICE([ Host system: $host_cpu-$host_vendor-$host_os])
AC_MSG_NOTICE([ Uname information: $UNAME_INFO])
AC_MSG_NOTICE([ Installation point: $prefix])
AC_MSG_NOTICE([ CFLAGS: $CFLAGS])
AC_MSG_NOTICE([ CPFLAGS: $CPPFLAGS $TLDEVEL_CPPFLAGS])
AC_MSG_NOTICE([ LDFLAGS: $LDFLAGS])
AC_MSG_NOTICE([ SIMD flags: $SIMD_FLAGS])
AC_MSG_NOTICE([---------------------------------------------------------])
kalign-3.3.1/dev/ 0000775 0000000 0000000 00000000000 14036164772 0013553 5 ustar 00root root 0000000 0000000 kalign-3.3.1/dev/Makefile.am 0000664 0000000 0000000 00000001241 14036164772 0015605 0 ustar 00root root 0000000 0000000 AUTOMAKE_OPTIONS = serial-tests
AM_COLOR_TESTS=always
EXTRA_DIST = \
run_io_test.sh \
run_aln_test.sh \
data/a2m.good.1 \
data/a2m.good.2 \
data/afa.good.1 \
data/afa.good.2 \
data/afa.good.3 \
data/clustal.good.1 \
data/clustal.good.2 \
data/BB11001.msf \
data/BB11001.tfa \
data/BB12006.msf \
data/BB12006.tfa \
data/BB30014.msf \
data/BB30014.tfa \
data/BB11001_EOF.msf
@VALGRIND_CHECK_RULES@
TESTS_ENVIRONMENT = \
myprog_abspath='$(top_srcdir)'/src/; \
export myprog_abspath;\
testdatafiledir='$(top_srcdir)'/dev/data/; \
export testdatafiledir;
TESTS = run_io_test.sh run_aln_test.sh
CLEANFILES = rwtest.clu rwtest.fasta rwtest.msf test.afa
kalign-3.3.1/dev/data/ 0000775 0000000 0000000 00000000000 14036164772 0014464 5 ustar 00root root 0000000 0000000 kalign-3.3.1/dev/data/BB11001.msf 0000664 0000000 0000000 00000001460 14036164772 0016042 0 ustar 00root root 0000000 0000000 PileUp
MSF: 96 Type: P Check: 7038 ..
Name: 1aab_ oo Len: 96 Check: 4681 Weight: 10.0
Name: 1j46_A oo Len: 96 Check: 1914 Weight: 10.0
Name: 1k99_A oo Len: 96 Check: 8221 Weight: 10.0
Name: 2lef_A oo Len: 96 Check: 2222 Weight: 10.0
//
1aab_ ...GKGDPKK PRGKMSSYAF FVQTSREEHK KKHPDASVNF SEFSKKCSER
1j46_A ......MQDR VKRPMNAFIV WSRDQRRKMA LENP..RMRN SEISKQLGYQ
1k99_A MKKLKKHPDF PKKPLTPYFR FFMEKRAKYA KLHP..EMSN LDLTKILSKK
2lef_A ........MH IKKPLNAFML YMKEMRANVV AEST..LKES AAINQILGRR
1aab_ WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGE.... ......
1j46_A WKMLTEAEKW PFFQEAQKLQ AMHREKYPNY KYRPRRKAKM LPK...
1k99_A YKELPEKKKM KYIQDFQREK QEFERNLARF REDHPDLIQN AKK...
2lef_A WHALSREEQA KYYELARKER QLHMQLYPGW SARDNYGKKK KRKREK
kalign-3.3.1/dev/data/BB11001.tfa 0000664 0000000 0000000 00000000600 14036164772 0016022 0 ustar 00root root 0000000 0000000 >1aab_
GKGDPKKPRGKMSSYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERWKT
MSAKEKGKFEDMAKADKARYEREMKTYIPPKGE
>1j46_A
MQDRVKRPMNAFIVWSRDQRRKMALENPRMRNSEISKQLGYQWKMLTEAE
KWPFFQEAQKLQAMHREKYPNYKYRPRRKAKMLPK
>1k99_A
MKKLKKHPDFPKKPLTPYFRFFMEKRAKYAKLHPEMSNLDLTKILSKKYK
ELPEKKKMKYIQDFQREKQEFERNLARFREDHPDLIQNAKK
>2lef_A
MHIKKPLNAFMLYMKEMRANVVAESTLKESAAINQILGRRWHALSREEQA
KYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK
kalign-3.3.1/dev/data/BB11001_EOF.msf 0000664 0000000 0000000 00000001451 14036164772 0016533 0 ustar 00root root 0000000 0000000 PileUp
MSF: 96 Type: P Check: 7038 ..
Name: 1aab_ oo Len: 96 Check: 4681 Weight: 10.0
Name: 1j46_A oo Len: 96 Check: 1914 Weight: 10.0
Name: 1k99_A oo Len: 96 Check: 8221 Weight: 10.0
Name: 2lef_A oo Len: 96 Check: 2222 Weight: 10.0
//
1aab_ ...GKGDPKK PRGKMSSYAF FVQTSREEHK KKHPDASVNF SEFSKKCSER
1j46_A ......MQDR VKRPMNAFIV WSRDQRRKMA LENP..RMRN SEISKQLGYQ
1k99_A MKKLKKHPDF PKKPLTPYFR FFMEKRAKYA KLHP..EMSN LDLTKILSKK
2lef_A ........MH IKKPLNAFML YMKEMRANVV AEST..LKES AAINQILGRR
1aab_ WKTMSAKEKG KFEDMAKADK ARYEREMKTY IPPKGE.... ......
1j46_A WKMLTEAEKW PFFQEAQKLQ AMHREKYPNY KYRPRRKAKM LPK...
1k99_A YKELPEKKKM KYIQDFQREK QEFERNLARF REDHPDLIQN AKK...
2lef_A WHALSREEQA KYYELARKER QLHMQLYPGW SARDNYGKKK KRKREK kalign-3.3.1/dev/data/BB12006.msf 0000664 0000000 0000000 00000003173 14036164772 0016053 0 ustar 00root root 0000000 0000000 PileUp
MSF: 245 Type: P Check: 59 ..
Name: 1al2_ad oo Len: 245 Check: 2091 Weight: 10.0
Name: 1bbt_ac oo Len: 245 Check: 8510 Weight: 10.0
Name: 1bev_ac oo Len: 245 Check: 6172 Weight: 10.0
Name: 1mec_ac oo Len: 245 Check: 3286 Weight: 10.0
//
1al2_ad .GLPVMNTPG SNQYLTADNF QSPCALPEFD VTPPIDIPGE VKNMMELAEI
1bbt_ac GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNQLPGR FTNLLDVAEA
1bev_ac .GLPTKPGPG SYQFMTTDED CSPCILPDFQ PTPEIFIPGK VNNLLEIAQV
1mec_ac SPIPVTIREH AGTWYSTLPD STVPIYGKTP VAPANYMVGE YKDFLEIAQI
1al2_ad D.TMIPFDLS ATKKNTMEMY RVRLSDKPHT DDPILCLSLS PASDPRLSHT
1bbt_ac CPTFLR.... ......FEGG VPYVTTKTDS DRVLAQFDMS LAA.KHMSNT
1bev_ac E.SILEANN. REGVEGVERY VIPVSVQDAL DAQIYALRLE LGGSGPLSSS
1mec_ac P.TFIG.... .NKMPNAVPY IEASNTAVK. TQPLAVYQVT LSC.SCLANT
1al2_ad MLGEILNYYT HWAGSLKFTF LFCGSMMATG KLLVSYAPPG ADPPKKRKEA
1bbt_ac FLAGLAQYYT QYSGTINLHF MFTGPTDAKA RYMVAYAPPG MEPPKTPEAA
1bev_ac LLGTLAKHYT QWSGSVEITC MFTGTFMTTG KVLLAYTPPG GDMPRNREEA
1mec_ac FLAALSRNFA QYRGSLVYTF VFTGTAMMKG KFLIAYTPPG AGKPTSRDQA
1al2_ad MLGTHVIWDI GLQSSCTMVV PWISNTTYRQ TIDD.....S FTEGGYISVF
1bbt_ac AHCIHAEWDT GLNSKFTFSI PYLSAADYTY TASDVAE..T TNVQGWVCLF
1bev_ac MLGTHVIWDF GLQSSITLVI PWISASHFRG VSNDDVLNYQ YYAAGHVTIW
1mec_ac MQATYAIWDL GLNSSYSFTV PFISPTHFRM VGTDQAN..I TNVDGWVTVW
1al2_ad YQTRIVVPLS TPREMDILGF VSACNDFSVR LLRDTTHIEQ KA...
1bbt_ac QITHGK.... .ADGDALVVL ASAGKDFELR LPVDARAE.. .....
1bev_ac YQTNMVIPPG FPNTAGIIMM IAAQPNFSFR IQKDREDMTQ TAILQ
1mec_ac QLTPLTYPPG CPTSAKILTM VSAGKDFSLK MPISPAPWSP Q....
kalign-3.3.1/dev/data/BB12006.tfa 0000664 0000000 0000000 00000001730 14036164772 0016035 0 ustar 00root root 0000000 0000000 >1al2_ad
GLPVMNTPGSNQYLTADNFQSPCALPEFDVTPPIDIPGEVKNMMELAEID
TMIPFDLSATKKNTMEMYRVRLSDKPHTDDPILCLSLSPASDPRLSHTML
GEILNYYTHWAGSLKFTFLFCGSMMATGKLLVSYAPPGADPPKKRKEAML
GTHVIWDIGLQSSCTMVVPWISNTTYRQTIDDSFTEGGYISVFYQTRIVV
PLSTPREMDILGFVSACNDFSVRLLRDTTHIEQKA
>1bbt_ac
GIFPVACSDGYGGLVTTDPKTADPVYGKVFNPPRNQLPGRFTNLLDVAEA
CPTFLRFEGGVPYVTTKTDSDRVLAQFDMSLAAKHMSNTFLAGLAQYYTQ
YSGTINLHFMFTGPTDAKARYMVAYAPPGMEPPKTPEAAAHCIHAEWDTG
LNSKFTFSIPYLSAADYTYTASDVAETTNVQGWVCLFQITHGKADGDALV
VLASAGKDFELRLPVDARAE
>1bev_ac
GLPTKPGPGSYQFMTTDEDCSPCILPDFQPTPEIFIPGKVNNLLEIAQVE
SILEANNREGVEGVERYVIPVSVQDALDAQIYALRLELGGSGPLSSSLLG
TLAKHYTQWSGSVEITCMFTGTFMTTGKVLLAYTPPGGDMPRNREEAMLG
THVIWDFGLQSSITLVIPWISASHFRGVSNDDVLNYQYYAAGHVTIWYQT
NMVIPPGFPNTAGIIMMIAAQPNFSFRIQKDREDMTQTAILQ
>1mec_ac
SPIPVTIREHAGTWYSTLPDSTVPIYGKTPVAPANYMVGEYKDFLEIAQI
PTFIGNKMPNAVPYIEASNTAVKTQPLAVYQVTLSCSCLANTFLAALSRN
FAQYRGSLVYTFVFTGTAMMKGKFLIAYTPPGAGKPTSRDQAMQATYAIW
DLGLNSSYSFTVPFISPTHFRMVGTDQANITNVDGWVTVWQLTPLTYPPG
CPTSAKILTMVSAGKDFSLKMPISPAPWSPQ
kalign-3.3.1/dev/data/BB30014.msf 0000664 0000000 0000000 00000054415 14036164772 0016057 0 ustar 00root root 0000000 0000000 PileUp
MSF: 307 Type: P Check: 2883 ..
Name: 1ags_A oo Len: 307 Check: 2542 Weight: 10.0
Name: GTA1_BOVIN oo Len: 307 Check: 1045 Weight: 10.0
Name: GTA1_MOUSE oo Len: 307 Check: 2301 Weight: 10.0
Name: GTC1_RAT oo Len: 307 Check: 6389 Weight: 10.0
Name: GTC_RABIT oo Len: 307 Check: 2138 Weight: 10.0
Name: GTA1_RABIT oo Len: 307 Check: 6143 Weight: 10.0
Name: GTA1_CAVPO oo Len: 307 Check: 2879 Weight: 10.0
Name: GTA3_RAT oo Len: 307 Check: 3064 Weight: 10.0
Name: GTA3_CHICK oo Len: 307 Check: 6404 Weight: 10.0
Name: GTA2_CHICK oo Len: 307 Check: 3444 Weight: 10.0
Name: GTA1_CHICK oo Len: 307 Check: 4246 Weight: 10.0
Name: GTA1_ANTST oo Len: 307 Check: 2040 Weight: 10.0
Name: GTA4_HUMAN oo Len: 307 Check: 7381 Weight: 10.0
Name: 1oe7_A oo Len: 307 Check: 3128 Weight: 10.0
Name: GTP1_BUFBU oo Len: 307 Check: 7779 Weight: 10.0
Name: GT28_SCHJA oo Len: 307 Check: 7618 Weight: 10.0
Name: GTS1_ASCSU oo Len: 307 Check: 6708 Weight: 10.0
Name: GTS9_CAEEL oo Len: 307 Check: 3425 Weight: 10.0
Name: GTS3_CAEEL oo Len: 307 Check: 9066 Weight: 10.0
Name: GTS5_CAEEL oo Len: 307 Check: 8451 Weight: 10.0
Name: GTS6_CAEEL oo Len: 307 Check: 245 Weight: 10.0
Name: GTS4_CAEEL oo Len: 307 Check: 1081 Weight: 10.0
Name: GTS2_CAEEL oo Len: 307 Check: 4110 Weight: 10.0
Name: GTS1_CAEEL oo Len: 307 Check: 1820 Weight: 10.0
Name: GTS_ANOGA oo Len: 307 Check: 660 Weight: 10.0
Name: GTS2_MANSE oo Len: 307 Check: 5117 Weight: 10.0
Name: GT1_ONCVO oo Len: 307 Check: 728 Weight: 10.0
Name: SC11_OMMSL oo Len: 307 Check: 7004 Weight: 10.0
Name: SC2_OCTDO oo Len: 307 Check: 9708 Weight: 10.0
Name: 1aw9_ oo Len: 307 Check: 4565 Weight: 10.0
Name: GTH3_ARATH oo Len: 307 Check: 2928 Weight: 10.0
Name: GTH7_ARATH oo Len: 307 Check: 2013 Weight: 10.0
Name: GTH6_ARATH oo Len: 307 Check: 8296 Weight: 10.0
Name: GTH_SILCU oo Len: 307 Check: 9759 Weight: 10.0
Name: GTH1_ARATH oo Len: 307 Check: 9980 Weight: 10.0
Name: GTH4_ARATH oo Len: 307 Check: 9350 Weight: 10.0
Name: GTH4_MAIZE oo Len: 307 Check: 3503 Weight: 10.0
Name: GTH1_MAIZE oo Len: 307 Check: 2572 Weight: 10.0
Name: GTH1_WHEAT oo Len: 307 Check: 9368 Weight: 10.0
Name: GTH5_ARATH oo Len: 307 Check: 9671 Weight: 10.0
Name: 1eem_A oo Len: 307 Check: 6005 Weight: 10.0
Name: GTO1_MOUSE oo Len: 307 Check: 911 Weight: 10.0
Name: GTO2_HUMAN oo Len: 307 Check: 9751 Weight: 10.0
Name: YKJ3_CAEEL oo Len: 307 Check: 7547 Weight: 10.0
//
1ags_A .......... .......... .......... ....AEKPKL H.YFNARGRM
GTA1_BOVIN .......... .......... .......... ....AGKPTL H.YFNGRGRM
GTA1_MOUSE .......... .......... .......... ....AGKPVL H.YFNARGRM
GTC1_RAT .......... .......... .......... ....PGKPVL H.YFDGRGRM
GTC_RABIT .......... .......... .......... ....AGKPKL H.YFNARGRM
GTA1_RABIT .......... .......... .......... ...MARKPLL H.YFNGRGRM
GTA1_CAVPO .......... .......... .......... ....SGKPVL H.YFNVQGRM
GTA3_RAT .......... .......... .......... ...MEVKPKL Y.YFQGRGRM
GTA3_CHICK .......... .......... .......... ....AAKPVL Y.YFNGRGKM
GTA2_CHICK .......... .......... .......... ...MAGKPKL H.YTRGRGKM
GTA1_CHICK .......... .......... .......... ...MSGKPVL H.YANTRGRM
GTA1_ANTST .......... .......... .......... ...MAGEQNI K.YFNIKGRM
GTA4_HUMAN .......... .......... .......... ...MAARPKL H.YPNGRGRM
1oe7_A .......... .......... .......... .....DHIKV I.YFNGRGRA
GTP1_BUFBU .......... .......... .......... .....PEYTI I.YFNARGRC
GT28_SCHJA .......... .......... .......... .......VKL I.YFNGRGRA
GTS1_ASCSU .......... .......... .......... .....PQYKL T.YFDIRGLG
GTS9_CAEEL .......... .......... .......... ....MVSYKL I.YFQSRGNG
GTS3_CAEEL .......... .......... .......... ....MVHYKL T.YFNARGLA
GTS5_CAEEL .......... .......... .......... ....MVSYKL T.YFNGRGAG
GTS6_CAEEL .......... .......... .......... ....MVHYKL V.YFPLRARA
GTS4_CAEEL .......... .......... .......... ....MPNYKL L.YFDARALA
GTS2_CAEEL .......... .......... .......... ....MVHYKL M.CFDVRGLG
GTS1_CAEEL .......... .......... .......... ....MPHFKF Y.YFDVRGRG
GTS_ANOGA .......... .........L SSSSISRSSL KCNIMPDYKV Y.YFNVKALG
GTS2_MANSE .......... .......... .......... ....MPKVVF H.YFGAKGWA
GT1_ONCVO FITMNFVVEA ASSNANQAIT SENSIKPKGK LQPQMEKYTL T.YFNGRGRA
SC11_OMMSL .......... .......... .......... ....MPSYTL Y.YFNGRGRA
SC2_OCTDO .......... .......... .......... ....MPSYTL N.YFNHRGRA
1aw9_ .......... .......... .......... .....APLKL Y.GMPLSPNV
GTH3_ARATH .......... .......... .......... ......VLTI Y..APLFASS
GTH7_ARATH .......... .......... .......... .....MVVKV Y.GQIKAANP
GTH6_ARATH .......... .......... .......... ....MASIKV H.GVPMSTAT
GTH_SILCU .......... .......... .......... ......TIKV H.GNPRSTAT
GTH1_ARATH .......... .......... .......... ....MAGIKV F.GHPASTAT
GTH4_ARATH .......... .......... .......... .....AGIKV F.GHPASIAT
GTH4_MAIZE .......... .......... .......... ...ATPAVKV Y.GWAISPFV
GTH1_MAIZE .......... .......... .......... .....APMKL Y.GAVMSWNL
GTH1_WHEAT .......... .......... .......... ....MSPVKV F.GHPMLTNV
GTH5_ARATH .......... .......... .......... ....MVTVKL Y.GMAYSTCT
1eem_A .......... ........SA RSLGKGSAPP GPVPEGSIRI Y.SMRFCPFA
GTO1_MOUSE .......... ....MSGESS RSLGKGSAPP GPVPEGQIRV Y.SMRFCPFA
GTO2_HUMAN .......... ....MSGDAT RTLGKGSQPP GPVPEGLIRI Y.SMRFCPYS
YKJ3_CAEEL .......... .......... MTVLAGVNSK IVKNGCWNHS YLQHAILPVA
1ags_A ESTRWLLAAA GVEFEEKFIK SAEDL...DK LRNDGYLMFQ QVPMVEIDG.
GTA1_BOVIN ECIRWLLAAA GVEFEEKFIE KPEDL...DK LKNDGSLMFQ QVPMVEIDG.
GTA1_MOUSE ECIRWLLAAA GVEFEEKFIQ SPEDL...EK LKKDGNLMFD QVPMVEIDG.
GTC1_RAT EPIRWLLAAA GVEFEEQFLK TRDDL...AR LRNDGSLMFQ QVPMVEIDG.
GTC_RABIT ESIRWLLTAA GVEFEEKCMK TREDL...EK LRKDGVLMFQ QVPMVEIDG.
GTA1_RABIT ESIRWLLAAA GEEFDEKFME TAEDL...DK LRNDGSLMYQ QVPMVEIDG.
GTA1_CAVPO ESIRWLLAAA GVEFEEKLIM CQEDL...DK LKNDGLLMFQ QVPMVEMDG.
GTA3_RAT ESIRWLLATA GVEFEEEFLE TREQY...EK LQKDGCLLFG QVPLVEIDG.
GTA3_CHICK ESIRWLLAAA GVEFEEVFLE TREQY...EK LLQSGILMFQ QVPMVEIDG.
GTA2_CHICK ESIRWLLAAA GVEFEEEFIE KKEDL...EK LRNDGSLLFQ QVPMVEIDG.
GTA1_CHICK ESVRWLLAAA GVEFEEKFLE KKEDL...QK LKSDGSLLFQ QVPMVEIDG.
GTA1_ANTST EAIRWLLAVA GVEFEEKFFE TKEQL...QK LKET.VLLFQ QVPMVEIDG.
GTA4_HUMAN ESVRWVLAAA GVEFDEEFLE TKEQL...YK LQDGNHLLFQ QVPMVEIDG.
1oe7_A ESIRMTLVAA GVNYEDERIS FQDW....PK IKP..TIPGG RLPAVKITDN
GTP1_BUFBU EAMRMLMADQ GAQWKEEVVT SDDWQ..KGD LKK..AAVYG QLPGFKDGD.
GT28_SCHJA EPIRMILVAA GVEFEDERIE FQDW....PK IKP..TIPGG RLPIVKITDK
GTS1_ASCSU EGARLIFHQA GVKFEDNRLK REDW....PA LKP..KTPFG QLPLLEVDG.
GTS9_CAEEL EIARQVFAFA GQEFIDERIS KEQW....AE IKN..MTPFG QVPVLEVDG.
GTS3_CAEEL EISRQLFHMA GVEFEDERIN EEKF....SQ LKP..TFPSG QVPILCIDG.
GTS5_CAEEL EVSRQIFAYA GQQYEDNRVT QEQW....PA LKETCAAPFG QLPFLEVDG.
GTS6_CAEEL EIARQIFAYA GQDYSEENLS FEQW....PA RKN..NTPFG QLPILEVDG.
GTS4_CAEEL EPIRIMFAML NVPYEDYRVS VEEW....SK LKP..TTPFG QLPILQVDG.
GTS2_CAEEL EVIRQLFYLG DVSFEDFRVS REEF....KS LKS..NLPSG QLPVLEIDG.
GTS1_CAEEL EAIRLLFHLA DEKFDDERFG MEQW....GV LKS..EMPLG QVPVLEIDG.
GTS_ANOGA EPLRFLLSYG NLPFDDVRIT REEW....PA LKP..TMPMR QMPVLEVDG.
GTS2_MANSE RP.TMLLAYG GQEFEDHRVE YEQW....PE FKP..NTPFG QMPVLEIDG.
GT1_ONCVO EVIRLLFALA NVSYEDNRIT RDEW....KY LKP..RTPFG HVPMLNVSG.
SC11_OMMSL EICRMLFAVA SVQYQDKRIE LAEW....TQ FKT..KMPCH MLPILEIDT.
SC2_OCTDO EICRMLFAAA GVQYNDRRIE TSEW....SN MRS..KMPCS MMPMLDIDN.
1aw9_ VRVATVLNEK GLDFEIVPVD LTTGAHKQPD FLA..LNPFG QIPALVDGD.
GTH3_ARATH KRAVVTLVEK GVSFETVNVD LMKGEQRQPE YLA..IQPFG KIPVLVDGD.
GTH7_ARATH QRVLLCFLEK DIEFEVIHVD LDKLEQKKPQ HLL..RQPFG QVPAIEDGY.
GTH6_ARATH MRVLATLYEK DLQFELIPVD MRAGAHKQEA HLA..LNPFG QIPALEDGD.
GTH_SILCU QRVLVALYEK HLEFEFVPID MGAGGHKQPS YLA..LNPFG QVPALEDGE.
GTH1_ARATH RRVLIALHEK NVDFEFVHVE LKDGEHKKEP FIL..RNPFG KVPAFEDGD.
GTH4_ARATH RRVLIALHEK NLDFELVHVE LKDGEHKKEP FLS..RNPFG QVPAFEDGD.
GTH4_MAIZE SRALLALEEA GVDYELVPMS RQDGDHRRPE HLA..RNPFG KVPVLEDGD.
GTH1_MAIZE TRCATALEEA GSDYEIVPIN FATAEHKSPE HLV..RNPFG QVPALQDGD.
GTH1_WHEAT ARVLLFLEEV GAEYELVPMD FVAGEHKRPQ HVQ..LNPFA KMPGFQDGD.
GTH5_ARATH KRVYTTAKEI GVDVKIVPVD LMKGEHKEPA YLDN.YHPFG VIPVLEDEDG
1eem_A ERTRLVLKAK GIRHEVININ LKNK...PEW FFK..KNPFG LVPVLENSQG
GTO1_MOUSE QRTLMVLKAK GIRHEVININ LKNK...PEW FFE..KNPLG LVPVLENSQG
GTO2_HUMAN HRTRLVLKAK DIRHEVVNIN LRNK...PEW YYT..KHPFG HIPVLETSQC
YKJ3_CAEEL QRALIYASVK NIPSDVINVH LQEKP...DW YFS..KHYKG QVPTLEHDEG
1ags_A ....MKLVQT RAILNYIASK YN.......L YRKDI...KE KALIDMYIEG
GTA1_BOVIN ....MKLVQT RAILNYIATK YN.......L YGKDM...KE RALIDMYSEG
GTA1_MOUSE ....MKLAQT RAILNYIATK YD.......L YGKDM...KE RALIDMYSEG
GTC1_RAT ....MKLVQT RAILNYIATK YN.......L YGKDM...KE RALIDMYAEG
GTC_RABIT ....MKLVQT RAIFNYIADK HN.......L YGKDI...KE RALIDMYTEG
GTA1_RABIT ....MKLVQT RAILNYVANK HN.......L YGKDM...KE RALIDMYTEG
GTA1_CAVPO ....MKMVQS RAILNYIATK YN.......L YGKDT...KE RLLIDMYTEG
GTA3_RAT ....MLLTQT RAILSYLAAK YN.......L YGKDL...KE RVRIDMYADG
GTA3_CHICK ....MKLVQT RAILNYIAGK YN.......L YGKDL...KE RALIDMYVGG
GTA2_CHICK ....MKMVQS RAILCYIAGK YN.......L YGKDL...KE RAWIDMYVEG
GTA1_CHICK ....MKMVQT RAILNYIAGK YN.......L YGKDL...KE RALIDMYVEG
GTA1_ANTST ....MKLVQT RAILHYIAEK YN.......L LGKDM...KE HAQIIMYSEG
GTA4_HUMAN ....MKLVQT RSILHYIADK HN.......L FGKNL...KE RTLIDMYVEG
1oe7_A HGHVKWMVES LAIARYMAKK HH.......M MGGTE...EE YYNVEKLIGQ
GTP1_BUFBU ....FTLYQS NAMLRLLARN HD.......L YGKNP...RE ASLIDMVNDG
GT28_SCHJA RGDVKTMSES LAIARFIARK HN.......M MGDTD...DE YYIIEKMIGQ
GTS1_ASCSU ....EVLAQS AAIYRYLGRQ FG.......L AGKTP...ME EAQVDSIFDQ
GTS9_CAEEL ....RQLAQS ITIVRYLSKQ FG.......I SGKSS...WE EAQVDALGDQ
GTS3_CAEEL ....AQFSQS TAIARYLARK FG.......F VGQTA...EE ELQADEVVDT
GTS5_CAEEL ....KKLAQS HAIARFLARE FK.......L NGKTA...WE EAQVNSLADQ
GTS6_CAEEL ....KPLGQS YAIARYLARE FG.......I AGQND...TE AAEVDAIADQ
GTS4_CAEEL ....EQFGQS MSITRYLARK FG.......L AGKTA...EE EAYADSIVDQ
GTS2_CAEEL ....VMISQS ASIGRFLARQ YG.......Y SGKTP...TE EMQVDSIIDL
GTS1_CAEEL ....VKISQT TAIARYLGHQ FH.......R AGTNA...VD CARLDMIAEV
GTS_ANOGA ....KRVHQS LAMCRYVAKQ IN.......L AGDNP...LE ALQIDAIVDT
GTS2_MANSE ....KKYAQS LAISRYLGRK YG.......L AGNDI...EE DFEIDQIVDF
GT1_ONCVO ....NVLGES HAIELLLGGR FG.......L LGTND...WE EAKIMAVVLN
SC11_OMMSL ...ETQVPQS MAISRYLARE FG.......F YGKNN...MD MFKVDCLCDS
SC2_OCTDO ...RHQIPQT MAIARYLARE FG.......F HGKNN...ME MARVEYISDC
1aw9_ ....EVLFES RAINRYIASK YASEG..TDL LPATA...SA AKL.EVWLEV
GTH3_ARATH ....YKIFES RAIMRYIAEK YRSQG..PDL LGKTI...EE RGQVEQWLDV
GTH7_ARATH ....LKLFES RAIARYYATK YADQG..TDL LGKTL...EG RAIVDQWVEV
GTH6_ARATH ....LTLFES RAITQYLAEE YSEKG..EKL ISQDCK..KV KATTNVWLQV
GTH_SILCU ....IKLFES RAITKYLAYT HDHQNEGTSL IHKEK...HE MAAQLVWEEV
GTH1_ARATH ....FKIFES RAITQYIAHE FSDKG..NNL LSTG....KD MAIIAMGIEI
GTH4_ARATH ....LKLFES RAITQYIAHR YENQGT..NL LQTDSKNISQ YAIMAIGMQV
GTH4_MAIZE ....LTLFES RAIARHVLRK HKP.....EL LGGGRL..EQ TAMVDVWLEV
GTH1_MAIZE ....LYLFES RAICKYAARK NKP.....EL LREGNL..EE AAMVDVWIEV
GTH1_WHEAT ....LVLFES RAIAKYILRK YGGTAG.LDL LGENSGI.EE LAMVDVWTEV
GTH5_ARATH ....TKIYES RAISRYLVAK YGKGS...SL LPSPSDP.KA YGLFEQAASV
1eem_A ....QLIYES AITCEYLDEA YPGKK....L LPDDP...YE KACQKMILEL
GTO1_MOUSE ....HLVTES VITCEYLDEA YPEK....KL FPDDP...YK KARQKMTLES
GTO2_HUMAN ....QLIYES VIACEYLDDA YPGR....KL FPYDP...YE RARQKMLLEL
YKJ3_CAEEL K...KHVIES AVIPEYLDDI YPET....RI LPTDP...YE KVQQKLLLDR
1ags_A .IADLGEMIL LLPFTQ.... ......PEEQ DAKLALIKEK IKNRYFPAFE
GTA1_BOVIN .VADLGEMIM HFPLCP.... ......PAEK DAKLTLIREK TTNRYLPAFE
GTA1_MOUSE .ILDLTEMIG QLVLCP.... ......PDQR EAKTALAKDR TKNRYLPAFE
GTC1_RAT .VADLDEIVL HYPYIP.... ......PGEK EASLAKIKDK ARNRYFPAFE
GTC_RABIT .IVDLNELIL TRPFLP.... ......PEEQ EAKLAQIKDK AKNRYFPAFE
GTA1_RABIT .VADLYELVL LLPLCP.... ......PEQK DAKVDFIKEK IRTRYFPAFE
GTA1_CAVPO .MTDLYELFF KVILAP.... ......PEEK DAAKSLIKDR AKNRFLPAFE
GTA3_RAT .TQDLMMMII GAPFKA.... ......PQEK EESLALAVKR AKNRYFPVFE
GTA3_CHICK .TDDLMGFLL SFPFLS.... ......AEDK VKQCAFVVEK ATSRYFPAYE
GTA2_CHICK .TTDLMGMIM ALPFQA.... ......ADVK EKNIALITER ATTRYFPVYE
GTA1_CHICK .LADLYELIM MNVVQP.... ......ADKK EEHLANALDK AANRYFPVFE
GTA1_ANTST .TMDLMELIM IYPFLK.... ......GEEK KQRLVEIANK AKGRYFPAFE
GTA4_HUMAN .TLDLLELLI MHPFLK.... ......PDDQ QKEVVNMAQK AIIRYFPVFE
1oe7_A .AEDLEHEYY KTLMKP.... ......EEEK QKIIKEILNG KVPVLLDIIC
GTP1_BUFBU .VEDLRLKYL KMIYQN.... .......... YENGKDDYVK ALPTNLGHFE
GT28_SCHJA .VEDVESEYH KTLIKP.... ......PEEK EKISKEILNG KVPILLQAIC
GTS1_ASCSU .FKDFMAELR PCFRVLAGFE ......EGDK EKVLKEVAVP ARDKHLPLLE
GTS9_CAEEL .FKDYRVEAR PFFRAKMGFS ......DGDV DQLYKDLFVP AFNKMYSIFT
GTS3_CAEEL .FKDFIESFR KFVIAVLSGE S.....EEIL KNIREEVIKP AVKTYTAYLK
GTS5_CAEEL .YKDYSSEAR PYFYAVMGFG ......PGDV ETLKKDIFLP AFEKFYGFLV
GTS6_CAEEL .FKDYLNDVS PYLTVLAGFK ......PGDK DQLRTDVFVP AFKKNFEFFE
GTS4_CAEEL .YRDFIFFFR QFTSSVFYGS D.....ADHI NKVRFEVVEP ARDDFLAIIN
GTS2_CAEEL .FKDFMLTFR QFFFAVIHGY P.....EYEK ERMKRDIVKP AIKNYFIALN
GTS1_CAEEL .IQEFMSSSG MGKFSRVLLG M....IQANK EQFFKENVLP DVEKYAPIVE
GTS_ANOGA .INDFRLKIA IVAYEPDD.. .......MVK EKKMVTLNNE VIPFYLTKLN
GTS2_MANSE .VNDIRASAA SVEYEQDAAN .........K EVKHEENMKN KYPFQLNKLS
GT1_ONCVO .IDELFQKLI PWTHEKNTTK .........K AELFRNLSES DVMPFLGRYE
SC11_OMMSL .LFELFNDYM AVYNEKDAA. .........K KTELQKRFQN TCLRVLPYME
SC2_OCTDO .FYDILDDYL RMYQDDNCRM MFQRSGDRNG SSEKRTRYQE TLRRILPFME
1aw9_ ESHHFYPNAS PLVFQLLVRP LLG....GAP DAAVVDKHAE QLAKVLDVYE
GTH3_ARATH EATSYHPPLL ALTLNIVFAP LMG....FPA DEKVIKESEE KLAEVLDVYE
GTH7_ARATH ENNYFYAVAL PLVMNVVFKP KSG....KPC DVALVEELKV KFDKVLDVYE
GTH6_ARATH EGQQFDPNAS KLAFERVFKG MFG....MTT DPAAVQELEG KLQKVLDVYE
GTH_SILCU EAHQFDPVAS KLAWELVFKG IFG....MQT DTTVVEENEA KLAKVLDVYE
GTH1_ARATH ESHEFDPVGS KLVWEQVLKP LYG....MTT DKTVVEEEEA KLAKVLDVYE
GTH4_ARATH EDHQFDPVAS KLAFEQIFKS IYG....LTT DEAVVAEEEA KLAKVLDVYE
GTH4_MAIZE EAHQLSPPAI AIVVECVFAP FLG....RER NQAVVDENVE KLKKVLEVYE
GTH1_MAIZE EANQYTAALN PILFQVLISP MLG....GTT DQKVVDENLE KLKKVLEVYE
GTH1_WHEAT EAQQYYPAIS PVVFECIIIP FIIPGGGAAP NQTVVDESLE RLRGVLGIYE
GTH5_ARATH EYSSFDPPAS SLAYERVFAG MRG....LKT NEELAKKYVD TLNAKMDGYE
1eem_A F.SKVPSLVG SFIRS..... .........Q NKEDYAGLKE EFRKEFTKLE
GTO1_MOUSE F.SKVPPLIA SFVRS..... .........K RKEDSPNLRE ALENEFKKLE
GTO2_HUMAN F.CKVPHLTK ECLVA..... ........LR CGRECTNLKA ALRQEFSNLE
YKJ3_CAEEL ISGQVSPAFY GVVQA..... ........VK NPDLREEKFA DIKKAYDNAE
1ags_A KVLKSHG..Q DYLVGNKL.S RADIHLVELL YYVEELDS.. .........S
GTA1_BOVIN NVLKSHG..Q DYLVGNKL.S RADIHLVELL YYVEELDP.. .........S
GTA1_MOUSE KVLKSHG..Q DYLVGNRL.T RVDIHLLEVL LYVEEFDA.. .........S
GTC1_RAT KVLKSHG..Q DYLVGNRL.S RADVYLVQVL YHVEELDP.. .........S
GTC_RABIT KVLKSHG..Q DYLVGNKL.S KADILLVELL YNVEELNP.. .........G
GTA1_RABIT KVLKSHG..Q DYLVGNRL.S KADILLVELL YNVEELDP.. .........S
GTA1_CAVPO KVLKSHG..Q GYLVGNKL.S KADILLTELL YMVEEFDA.. .........S
GTA3_RAT KILKDHG..E AFLVGNQL.S WADIQLLEAI LMVEEVSA.. .........P
GTA3_CHICK KVLKDHG..Q DFLVGNRL.S WADIHLLEAI LMVEEKKS.. .........D
GTA2_CHICK KALKDHG..Q DYLVGNKL.S WADIHLLEAI LMTEELKS.. .........D
GTA1_CHICK KVLKDHG..H DFLVGNKL.S RADVHLLETI LAVEESKP.. .........D
GTA1_ANTST NVLKTHG..Q NFLVGNQL.S MADVQLFEAI LMVEEKVP.. .........D
GTA4_HUMAN KILRGHG..Q SFLVGNQL.S LADVILLQTI LALEEKIP.. .........N
1oe7_A ESLKAST..G KLAVGDKV.T LADLVLIAVI DHVTDLDK.. ........EF
GTP1_BUFBU RLLASNNEGK GFVVGAHI.S FADYNLVDLL HNHLVLAP.. .........D
GT28_SCHJA ETLKEST..G NLTVGDKV.T LADVVLIASI DHITDLDK.. ........EF
GTS1_ASCSU KFLAKSG..S EYMVGKSV.T WADLVITDSL ASWESLIP.. .........D
GTS9_CAEEL ESLKSSG..S GFLVGDSL.T WMDLAIAQHS ADLLEADG.. .........K
GTS3_CAEEL AILEKSS..S GYLVGNEL.T WADLVIADNL TTLINAEL.. .........L
GTS5_CAEEL NFLKASG..S GFLVGDSL.T WIDLAIAQHS ADLIAKGG.. ..........
GTS6_CAEEL NILASNHS.. GFFVGNSL.T WVDLLISQHV QDILDKDL.. .........A
GTS4_CAEEL KFLAKSK..S GFLVGDSL.T WADIVIADNL TSLLKNGF.. .........L
GTS2_CAEEL KILLRSK..S GFLVGDDL.T WADLQIADNL STLINIRL.. ..........
GTS1_CAEEL KFLLENGN.N GLLLGDRE.T WVDVFAAESF SKLIDYGSP. .........D
GTS_ANOGA VIAKENN... GHLVLGKP.T WADVYFAGIL DYLNYLTKT. .........N
GTS2_MANSE EIITKNN... GFLALGRL.T WADFVFVGMF DYLKKMLR.. .......MPD
GT1_ONCVO KFLKEST..T GHIVGNKV.S VADLTVFNML MTLDDEVK.. ..........
SC11_OMMSL KTLEANKGGA GWFIGDQI.L LCDMMTHAAL ENPIQENAN. ..........
SC2_OCTDO RTLEMYKSGG QFFMGDQM.T MADMMCYCAL ENPIMEES.. .........S
1aw9_ AHLARN.... KYLAGDEF.T LADANHASYL LYLSKTPK.. ........AG
GTH3_ARATH AQLSKNE... .YLAGDFV.S LADLAHLPFT EYLVGPIG.. .......KAH
GTH7_ARATH NRLATNR... .YLGGDEF.T LADLSHMPGM RYIMNETS.. .......LSG
GTH6_ARATH ARLAKSE... .FLAGDSF.T LADLHHLPAI HYLLGTDS.. ........KV
GTH_SILCU ARLTESEY.. .LGANDSF.T LVDLHHLPLL GYLMGTQV.. ........KK
GTH1_ARATH HRLGESK... .YLASDHF.T LVDLHTIPVI QYLLGTPT.. ........KK
GTH4_ARATH ARLKEFK... .YLAGETF.T LTDLHHIPAI QYLLGTPT.. ........KK
GTH4_MAIZE ARLATCT... .YLAGDFL.S LADLSPFTIM HCLMATEY.. ........AA
GTH1_MAIZE ARLTKCK... .YLAGDFL.S LADLNHVSVT LCLFATPY.. ........AS
GTH1_WHEAT ARLEKSR... .YLAGDSI.T FADLNHIPFT FYFMTTPY.. ........AK
GTH5_ARATH RILSKQK... .YLAGNDF.T LADLFHLPYG AMVAQLEP.. .........T
1eem_A EVLTNKK..T TFFGGNSI.S MIDYLIWPWF ERLEAMKLN. .........E
GTO1_MOUSE EGMDNYK... SFLGGDSP.S MVDYLTWPWF QRLEALELK. .........E
GTO2_HUMAN EILEYQN..T TFFGGTCI.S MIDYLLWPWF ERLDVYGIL. .........D
YKJ3_CAEEL QLLTGD.... .FYSGTSKPG FVDYLLYPNI QRAYWAAHIV PDFPLEAESF
1ags_A LISSFPLLKA LKTRISN.LP TVKKFLQPGS PRKPPMDEKS LEEARKIFRF
GTA1_BOVIN LLANFPLLKA LKARVSS.LP AVKKFLQPGS QRKPPTDEKK IEEARKVFKF
GTA1_MOUSE LLTPFPLLKA FKSRISS.LP NVKKFLQPGS QRKPPMDAKQ IQEARKAFKI
GTC1_RAT ALANFPLLKA LRTRVSN.LP TVKKFLQPGS QRKPLEDEKC VESAVKIFS.
GTC_RABIT ATASFPLLQA LKTRISN.LP TVKKFLQPGS QRNPPDDEKC REEAKIIFH.
GTA1_RABIT AIASFPLLKA LKTRISS.LP TVKKFLQPGS QRKPPMDEKN LEKAKKIFKI
GTA1_CAVPO LLANFTLLQA LKTRVSN.LP NVKKFLQPGS QRKPFPTQEM FEEMRKF...
GTA3_RAT VLSDFPLLQA FKTRISN.IP TIKKFLQPGS QRKPPPDGHY VDVVRTVLKF
GTA3_CHICK ALSGFPLLQA FKKRISS.IP TIKKFLAPGS KRKPISDDKY VETVRRVLRM
GTA2_CHICK ILSAFPLLQA FKGRMSN.VP TIKKFLQPGS QRKPPLDEKS IANVRKIFSF
GTA1_CHICK ALAKFPLLQS FKARTSN.IP NIKKFLQPGS QRKPRLEEKD IPRLMAIFH.
GTA1_ANTST ALSGFPLLQA FKTRISN.IP TVKTFLAPGS KRKPVPDAKY VEDIIKIFYF
GTA4_HUMAN ILSAFPFLQE YTVKLSN.IP TIKRFLEPGS KKKPPPDEIY VRTVYNIFRP
1oe7_A LTGKYPEIHK HRENLLASSP RLAKYLSDRA .......... ..........
GTP1_BUFBU CLSGFPLLCA YVKRISS.RP KLEAYLSSDA HKKRPINGNG KQQ.......
GT28_SCHJA LTGKYPEIHK HRKHLLATSP KLAKYLSERH ATAF...... ..........
GTS1_ASCSU FLSGHLQLKK YIEHVRE.LP NIKKWIAERP KTPY...... ..........
GTS9_CAEEL ILDTFLEMKD HQKKIHS.IP NVKKWIEKRP VTSR...... ..........
GTS3_CAEEL DIENDKLLKE FREKIIE.TP KLKEWLAKRP ETRF...... ..........
GTS5_CAEEL DFSKFPELKA HAEKIQA.IP QIKKWIETRP VTPF...... ..........
GTS6_CAEEL VVEEFKKVLA HRKKVQS.ID RIQKYIANRP DYPF...... ..........
GTS4_CAEEL DFNKEKKLEE FYNKIHS.IP EIKNYVATRK DSIV...... ..........
GTS2_CAEEL FAEKEPHLNV FIRKL..... .......... .......... ..........
GTS1_CAEEL ALDAYPHILA LINRVFN.HP NIKKYVSQRK ATPA...... ..........
GTS_ANOGA LLENFPNLQE VVQKVLD.NE NVKAYIAKRP ITEV...... ..........
GTS2_MANSE LEEQYPIFKK PIETVLS.NP KLKAYLDSAP KKEF...... ..........
GT1_ONCVO .LEEYPQLAS FVNKIGQ.MP GIKEWIKKRP KTYF...... ..........
SC11_OMMSL LLKEYPKLAA LRTRVAA.HP KIAAYIKKRN NTAF...... ..........
SC2_OCTDO LLNSYPKLQA LRTRVMS.HL KMSPYLKKRS STEF...... ..........
1aw9_ LVAARPHVKA WWEAIVA.RP AFQKTVAAIP LPPPP..... ..........
GTH3_ARATH LIKDRKHVSA WWDKISS.RA AWKEVSAKYS LPV....... ..........
GTH7_ARATH LVTSRENLNR WWNEISA.RP AWKKLMELAA Y......... ..........
GTH6_ARATH LFDSRPKVSE WIKKISA.RP AWAKVIDLQK Q......... ..........
GTH_SILCU LFEERAHVSA WCKKILA.RP SWEKTLALQK QA........ ..........
GTH1_ARATH LFDERPHVSA WVADITS.RP SAQKVL.... .......... ..........
GTH4_ARATH LFTERPRVNE WVAEITK.RP ASEKVQ.... .......... ..........
GTH4_MAIZE LVHALPHVSA WWQGLAA.RP AANKVAQFMP VGAGAPKEQE ..........
GTH1_MAIZE VLDAYPHVKA WWSGLME.RP SVQKVAALMK PSA....... ..........
GTH1_WHEAT VFDDYPKVKA WWEMLMA.RP AVQRVCKHMP TEFKLGAQY. ..........
GTH5_ARATH VLDSKPHVKA WWAASLRVIP GRLLRNSSKE FM........ ..........
1eem_A CVDHTPKLKL WMAAMKE.DP TVSALLTSEK DWQGFLELYL QNSPEACDYG
GTO1_MOUSE CLAHTPKLKL WMAAMQQ.DP VASSHKIDAK TYREYLNLYL QDSPEACDYG
GTO2_HUMAN CVSHTPALRL WISAMKW.DP TVCALLMDKS IFQGFLNLYF QNNPNAFDFG
YKJ3_CAEEL PGPNYPRLSK WYKALESIPE VAAASQPTEN GVGFFKDYLG GSPNYDYGLT
1ags_A .......
GTA1_BOVIN .......
GTA1_MOUSE Q......
GTC1_RAT .......
GTC_RABIT .......
GTA1_RABIT P......
GTA1_CAVPO .......
GTA3_RAT .......
GTA3_CHICK YYDVKPH
GTA2_CHICK .......
GTA1_CHICK .......
GTA1_ANTST .......
GTA4_HUMAN .......
1oe7_A .......
GTP1_BUFBU .......
GT28_SCHJA .......
GTS1_ASCSU .......
GTS9_CAEEL .......
GTS3_CAEEL .......
GTS5_CAEEL .......
GTS6_CAEEL .......
GTS4_CAEEL .......
GTS2_CAEEL .......
GTS1_CAEEL .......
GTS_ANOGA .......
GTS2_MANSE .......
GT1_ONCVO .......
SC11_OMMSL .......
SC2_OCTDO .......
1aw9_ .......
GTH3_ARATH .......
GTH7_ARATH .......
GTH6_ARATH .......
GTH_SILCU .......
GTH1_ARATH .......
GTH4_ARATH .......
GTH4_MAIZE .......
GTH1_MAIZE .......
GTH1_WHEAT .......
GTH5_ARATH .......
1eem_A L......
GTO1_MOUSE L......
GTO2_HUMAN LC.....
YKJ3_CAEEL KLSETI.
kalign-3.3.1/dev/data/BB30014.tfa 0000664 0000000 0000000 00000024054 14036164772 0016040 0 ustar 00root root 0000000 0000000 >1ags_A
AEKPKLHYFNARGRMESTRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLM
FQQVPMVEIDGMKLVQTRAILNYIASKYNLYRKDIKEKALIDMYIEGIAD
LGEMILLLPFTQPEEQDAKLALIKEKIKNRYFPAFEKVLKSHGQDYLVGN
KLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPG
SPRKPPMDEKSLEEARKIFRF
>GTA1_BOVIN
AGKPTLHYFNGRGRMECIRWLLAAAGVEFEEKFIEKPEDLDKLKNDGSLM
FQQVPMVEIDGMKLVQTRAILNYIATKYNLYGKDMKERALIDMYSEGVAD
LGEMIMHFPLCPPAEKDAKLTLIREKTTNRYLPAFENVLKSHGQDYLVGN
KLSRADIHLVELLYYVEELDPSLLANFPLLKALKARVSSLPAVKKFLQPG
SQRKPPTDEKKIEEARKVFKF
>GTA1_MOUSE
AGKPVLHYFNARGRMECIRWLLAAAGVEFEEKFIQSPEDLEKLKKDGNLM
FDQVPMVEIDGMKLAQTRAILNYIATKYDLYGKDMKERALIDMYSEGILD
LTEMIGQLVLCPPDQREAKTALAKDRTKNRYLPAFEKVLKSHGQDYLVGN
RLTRVDIHLLEVLLYVEEFDASLLTPFPLLKAFKSRISSLPNVKKFLQPG
SQRKPPMDAKQIQEARKAFKIQ
>GTC1_RAT
PGKPVLHYFDGRGRMEPIRWLLAAAGVEFEEQFLKTRDDLARLRNDGSLM
FQQVPMVEIDGMKLVQTRAILNYIATKYNLYGKDMKERALIDMYAEGVAD
LDEIVLHYPYIPPGEKEASLAKIKDKARNRYFPAFEKVLKSHGQDYLVGN
RLSRADVYLVQVLYHVEELDPSALANFPLLKALRTRVSNLPTVKKFLQPG
SQRKPLEDEKCVESAVKIFS
>GTC_RABIT
AGKPKLHYFNARGRMESIRWLLTAAGVEFEEKCMKTREDLEKLRKDGVLM
FQQVPMVEIDGMKLVQTRAIFNYIADKHNLYGKDIKERALIDMYTEGIVD
LNELILTRPFLPPEEQEAKLAQIKDKAKNRYFPAFEKVLKSHGQDYLVGN
KLSKADILLVELLYNVEELNPGATASFPLLQALKTRISNLPTVKKFLQPG
SQRNPPDDEKCREEAKIIFH
>GTA1_RABIT
MARKPLLHYFNGRGRMESIRWLLAAAGEEFDEKFMETAEDLDKLRNDGSL
MYQQVPMVEIDGMKLVQTRAILNYVANKHNLYGKDMKERALIDMYTEGVA
DLYELVLLLPLCPPEQKDAKVDFIKEKIRTRYFPAFEKVLKSHGQDYLVG
NRLSKADILLVELLYNVEELDPSAIASFPLLKALKTRISSLPTVKKFLQP
GSQRKPPMDEKNLEKAKKIFKIP
>GTA1_CAVPO
SGKPVLHYFNVQGRMESIRWLLAAAGVEFEEKLIMCQEDLDKLKNDGLLM
FQQVPMVEMDGMKMVQSRAILNYIATKYNLYGKDTKERLLIDMYTEGMTD
LYELFFKVILAPPEEKDAAKSLIKDRAKNRFLPAFEKVLKSHGQGYLVGN
KLSKADILLTELLYMVEEFDASLLANFTLLQALKTRVSNLPNVKKFLQPG
SQRKPFPTQEMFEEMRKF
>GTA3_RAT
MEVKPKLYYFQGRGRMESIRWLLATAGVEFEEEFLETREQYEKLQKDGCL
LFGQVPLVEIDGMLLTQTRAILSYLAAKYNLYGKDLKERVRIDMYADGTQ
DLMMMIIGAPFKAPQEKEESLALAVKRAKNRYFPVFEKILKDHGEAFLVG
NQLSWADIQLLEAILMVEEVSAPVLSDFPLLQAFKTRISNIPTIKKFLQP
GSQRKPPPDGHYVDVVRTVLKF
>GTA3_CHICK
AAKPVLYYFNGRGKMESIRWLLAAAGVEFEEVFLETREQYEKLLQSGILM
FQQVPMVEIDGMKLVQTRAILNYIAGKYNLYGKDLKERALIDMYVGGTDD
LMGFLLSFPFLSAEDKVKQCAFVVEKATSRYFPAYEKVLKDHGQDFLVGN
RLSWADIHLLEAILMVEEKKSDALSGFPLLQAFKKRISSIPTIKKFLAPG
SKRKPISDDKYVETVRRVLRMYYDVKPH
>GTA2_CHICK
MAGKPKLHYTRGRGKMESIRWLLAAAGVEFEEEFIEKKEDLEKLRNDGSL
LFQQVPMVEIDGMKMVQSRAILCYIAGKYNLYGKDLKERAWIDMYVEGTT
DLMGMIMALPFQAADVKEKNIALITERATTRYFPVYEKALKDHGQDYLVG
NKLSWADIHLLEAILMTEELKSDILSAFPLLQAFKGRMSNVPTIKKFLQP
GSQRKPPLDEKSIANVRKIFSF
>GTA1_CHICK
MSGKPVLHYANTRGRMESVRWLLAAAGVEFEEKFLEKKEDLQKLKSDGSL
LFQQVPMVEIDGMKMVQTRAILNYIAGKYNLYGKDLKERALIDMYVEGLA
DLYELIMMNVVQPADKKEEHLANALDKAANRYFPVFEKVLKDHGHDFLVG
NKLSRADVHLLETILAVEESKPDALAKFPLLQSFKARTSNIPNIKKFLQP
GSQRKPRLEEKDIPRLMAIFH
>GTA1_ANTST
MAGEQNIKYFNIKGRMEAIRWLLAVAGVEFEEKFFETKEQLQKLKETVLL
FQQVPMVEIDGMKLVQTRAILHYIAEKYNLLGKDMKEHAQIIMYSEGTMD
LMELIMIYPFLKGEEKKQRLVEIANKAKGRYFPAFENVLKTHGQNFLVGN
QLSMADVQLFEAILMVEEKVPDALSGFPLLQAFKTRISNIPTVKTFLAPG
SKRKPVPDAKYVEDIIKIFYF
>GTA4_HUMAN
MAARPKLHYPNGRGRMESVRWVLAAAGVEFDEEFLETKEQLYKLQDGNHL
LFQQVPMVEIDGMKLVQTRSILHYIADKHNLFGKNLKERTLIDMYVEGTL
DLLELLIMHPFLKPDDQQKEVVNMAQKAIIRYFPVFEKILRGHGQSFLVG
NQLSLADVILLQTILALEEKIPNILSAFPFLQEYTVKLSNIPTIKRFLEP
GSKKKPPPDEIYVRTVYNIFRP
>1oe7_A
DHIKVIYFNGRGRAESIRMTLVAAGVNYEDERISFQDWPKIKPTIPGGRL
PAVKITDNHGHVKWMVESLAIARYMAKKHHMMGGTEEEYYNVEKLIGQAE
DLEHEYYKTLMKPEEEKQKIIKEILNGKVPVLLDIICESLKASTGKLAVG
DKVTLADLVLIAVIDHVTDLDKEFLTGKYPEIHKHRENLLASSPRLAKYL
SDRA
>GTP1_BUFBU
PEYTIIYFNARGRCEAMRMLMADQGAQWKEEVVTSDDWQKGDLKKAAVYG
QLPGFKDGDFTLYQSNAMLRLLARNHDLYGKNPREASLIDMVNDGVEDLR
LKYLKMIYQNYENGKDDYVKALPTNLGHFERLLASNNEGKGFVVGAHISF
ADYNLVDLLHNHLVLAPDCLSGFPLLCAYVKRISSRPKLEAYLSSDAHKK
RPINGNGKQQ
>GT28_SCHJA
VKLIYFNGRGRAEPIRMILVAAGVEFEDERIEFQDWPKIKPTIPGGRLPI
VKITDKRGDVKTMSESLAIARFIARKHNMMGDTDDEYYIIEKMIGQVEDV
ESEYHKTLIKPPEEKEKISKEILNGKVPILLQAICETLKESTGNLTVGDK
VTLADVVLIASIDHITDLDKEFLTGKYPEIHKHRKHLLATSPKLAKYLSE
RHATAF
>GTS1_ASCSU
PQYKLTYFDIRGLGEGARLIFHQAGVKFEDNRLKREDWPALKPKTPFGQL
PLLEVDGEVLAQSAAIYRYLGRQFGLAGKTPMEEAQVDSIFDQFKDFMAE
LRPCFRVLAGFEEGDKEKVLKEVAVPARDKHLPLLEKFLAKSGSEYMVGK
SVTWADLVITDSLASWESLIPDFLSGHLQLKKYIEHVRELPNIKKWIAER
PKTPY
>GTS9_CAEEL
MVSYKLIYFQSRGNGEIARQVFAFAGQEFIDERISKEQWAEIKNMTPFGQ
VPVLEVDGRQLAQSITIVRYLSKQFGISGKSSWEEAQVDALGDQFKDYRV
EARPFFRAKMGFSDGDVDQLYKDLFVPAFNKMYSIFTESLKSSGSGFLVG
DSLTWMDLAIAQHSADLLEADGKILDTFLEMKDHQKKIHSIPNVKKWIEK
RPVTSR
>GTS3_CAEEL
MVHYKLTYFNARGLAEISRQLFHMAGVEFEDERINEEKFSQLKPTFPSGQ
VPILCIDGAQFSQSTAIARYLARKFGFVGQTAEEELQADEVVDTFKDFIE
SFRKFVIAVLSGESEEILKNIREEVIKPAVKTYTAYLKAILEKSSSGYLV
GNELTWADLVIADNLTTLINAELLDIENDKLLKEFREKIIETPKLKEWLA
KRPETRF
>GTS5_CAEEL
MVSYKLTYFNGRGAGEVSRQIFAYAGQQYEDNRVTQEQWPALKETCAAPF
GQLPFLEVDGKKLAQSHAIARFLAREFKLNGKTAWEEAQVNSLADQYKDY
SSEARPYFYAVMGFGPGDVETLKKDIFLPAFEKFYGFLVNFLKASGSGFL
VGDSLTWIDLAIAQHSADLIAKGGDFSKFPELKAHAEKIQAIPQIKKWIE
TRPVTPF
>GTS6_CAEEL
MVHYKLVYFPLRARAEIARQIFAYAGQDYSEENLSFEQWPARKNNTPFGQ
LPILEVDGKPLGQSYAIARYLAREFGIAGQNDTEAAEVDAIADQFKDYLN
DVSPYLTVLAGFKPGDKDQLRTDVFVPAFKKNFEFFENILASNHSGFFVG
NSLTWVDLLISQHVQDILDKDLAVVEEFKKVLAHRKKVQSIDRIQKYIAN
RPDYPF
>GTS4_CAEEL
MPNYKLLYFDARALAEPIRIMFAMLNVPYEDYRVSVEEWSKLKPTTPFGQ
LPILQVDGEQFGQSMSITRYLARKFGLAGKTAEEEAYADSIVDQYRDFIF
FFRQFTSSVFYGSDADHINKVRFEVVEPARDDFLAIINKFLAKSKSGFLV
GDSLTWADIVIADNLTSLLKNGFLDFNKEKKLEEFYNKIHSIPEIKNYVA
TRKDSIV
>GTS2_CAEEL
MVHYKLMCFDVRGLGEVIRQLFYLGDVSFEDFRVSREEFKSLKSNLPSGQ
LPVLEIDGVMISQSASIGRFLARQYGYSGKTPTEEMQVDSIIDLFKDFML
TFRQFFFAVIHGYPEYEKERMKRDIVKPAIKNYFIALNKILLRSKSGFLV
GDDLTWADLQIADNLSTLINIRLFAEKEPHLNVFIRKL
>GTS1_CAEEL
MPHFKFYYFDVRGRGEAIRLLFHLADEKFDDERFGMEQWGVLKSEMPLGQ
VPVLEIDGVKISQTTAIARYLGHQFHRAGTNAVDCARLDMIAEVIQEFMS
SSGMGKFSRVLLGMIQANKEQFFKENVLPDVEKYAPIVEKFLLENGNNGL
LLGDRETWVDVFAAESFSKLIDYGSPDALDAYPHILALINRVFNHPNIKK
YVSQRKATPA
>GTS_ANOGA
LSSSSISRSSLKCNIMPDYKVYYFNVKALGEPLRFLLSYGNLPFDDVRIT
REEWPALKPTMPMRQMPVLEVDGKRVHQSLAMCRYVAKQINLAGDNPLEA
LQIDAIVDTINDFRLKIAIVAYEPDDMVKEKKMVTLNNEVIPFYLTKLNV
IAKENNGHLVLGKPTWADVYFAGILDYLNYLTKTNLLENFPNLQEVVQKV
LDNENVKAYIAKRPITEV
>GTS2_MANSE
MPKVVFHYFGAKGWARPTMLLAYGGQEFEDHRVEYEQWPEFKPNTPFGQM
PVLEIDGKKYAQSLAISRYLGRKYGLAGNDIEEDFEIDQIVDFVNDIRAS
AASVEYEQDAANKEVKHEENMKNKYPFQLNKLSEIITKNNGFLALGRLTW
ADFVFVGMFDYLKKMLRMPDLEEQYPIFKKPIETVLSNPKLKAYLDSAPK
KEF
>GT1_ONCVO
FITMNFVVEAASSNANQAITSENSIKPKGKLQPQMEKYTLTYFNGRGRAE
VIRLLFALANVSYEDNRITRDEWKYLKPRTPFGHVPMLNVSGNVLGESHA
IELLLGGRFGLLGTNDWEEAKIMAVVLNIDELFQKLIPWTHEKNTTKKAE
LFRNLSESDVMPFLGRYEKFLKESTTGHIVGNKVSVADLTVFNMLMTLDD
EVKLEEYPQLASFVNKIGQMPGIKEWIKKRPKTYF
>SC11_OMMSL
MPSYTLYYFNGRGRAEICRMLFAVASVQYQDKRIELAEWTQFKTKMPCHM
LPILEIDTETQVPQSMAISRYLAREFGFYGKNNMDMFKVDCLCDSLFELF
NDYMAVYNEKDAAKKTELQKRFQNTCLRVLPYMEKTLEANKGGAGWFIGD
QILLCDMMTHAALENPIQENANLLKEYPKLAALRTRVAAHPKIAAYIKKR
NNTAF
>SC2_OCTDO
MPSYTLNYFNHRGRAEICRMLFAAAGVQYNDRRIETSEWSNMRSKMPCSM
MPMLDIDNRHQIPQTMAIARYLAREFGFHGKNNMEMARVEYISDCFYDIL
DDYLRMYQDDNCRMMFQRSGDRNGSSEKRTRYQETLRRILPFMERTLEMY
KSGGQFFMGDQMTMADMMCYCALENPIMEESSLLNSYPKLQALRTRVMSH
LKMSPYLKKRSSTEF
>1aw9_
APLKLYGMPLSPNVVRVATVLNEKGLDFEIVPVDLTTGAHKQPDFLALNP
FGQIPALVDGDEVLFESRAINRYIASKYASEGTDLLPATASAAKLEVWLE
VESHHFYPNASPLVFQLLVRPLLGGAPDAAVVDKHAEQLAKVLDVYEAHL
ARNKYLAGDEFTLADANHASYLLYLSKTPKAGLVAARPHVKAWWEAIVAR
PAFQKTVAAIPLPPPP
>GTH3_ARATH
VLTIYAPLFASSKRAVVTLVEKGVSFETVNVDLMKGEQRQPEYLAIQPFG
KIPVLVDGDYKIFESRAIMRYIAEKYRSQGPDLLGKTIEERGQVEQWLDV
EATSYHPPLLALTLNIVFAPLMGFPADEKVIKESEEKLAEVLDVYEAQLS
KNEYLAGDFVSLADLAHLPFTEYLVGPIGKAHLIKDRKHVSAWWDKISSR
AAWKEVSAKYSLPV
>GTH7_ARATH
MVVKVYGQIKAANPQRVLLCFLEKDIEFEVIHVDLDKLEQKKPQHLLRQP
FGQVPAIEDGYLKLFESRAIARYYATKYADQGTDLLGKTLEGRAIVDQWV
EVENNYFYAVALPLVMNVVFKPKSGKPCDVALVEELKVKFDKVLDVYENR
LATNRYLGGDEFTLADLSHMPGMRYIMNETSLSGLVTSRENLNRWWNEIS
ARPAWKKLMELAAY
>GTH6_ARATH
MASIKVHGVPMSTATMRVLATLYEKDLQFELIPVDMRAGAHKQEAHLALN
PFGQIPALEDGDLTLFESRAITQYLAEEYSEKGEKLISQDCKKVKATTNV
WLQVEGQQFDPNASKLAFERVFKGMFGMTTDPAAVQELEGKLQKVLDVYE
ARLAKSEFLAGDSFTLADLHHLPAIHYLLGTDSKVLFDSRPKVSEWIKKI
SARPAWAKVIDLQKQ
>GTH_SILCU
TIKVHGNPRSTATQRVLVALYEKHLEFEFVPIDMGAGGHKQPSYLALNPF
GQVPALEDGEIKLFESRAITKYLAYTHDHQNEGTSLIHKEKHEMAAQLVW
EEVEAHQFDPVASKLAWELVFKGIFGMQTDTTVVEENEAKLAKVLDVYEA
RLTESEYLGANDSFTLVDLHHLPLLGYLMGTQVKKLFEERAHVSAWCKKI
LARPSWEKTLALQKQA
>GTH1_ARATH
MAGIKVFGHPASTATRRVLIALHEKNVDFEFVHVELKDGEHKKEPFILRN
PFGKVPAFEDGDFKIFESRAITQYIAHEFSDKGNNLLSTGKDMAIIAMGI
EIESHEFDPVGSKLVWEQVLKPLYGMTTDKTVVEEEEAKLAKVLDVYEHR
LGESKYLASDHFTLVDLHTIPVIQYLLGTPTKKLFDERPHVSAWVADITS
RPSAQKVL
>GTH4_ARATH
AGIKVFGHPASIATRRVLIALHEKNLDFELVHVELKDGEHKKEPFLSRNP
FGQVPAFEDGDLKLFESRAITQYIAHRYENQGTNLLQTDSKNISQYAIMA
IGMQVEDHQFDPVASKLAFEQIFKSIYGLTTDEAVVAEEEAKLAKVLDVY
EARLKEFKYLAGETFTLTDLHHIPAIQYLLGTPTKKLFTERPRVNEWVAE
ITKRPASEKVQ
>GTH4_MAIZE
ATPAVKVYGWAISPFVSRALLALEEAGVDYELVPMSRQDGDHRRPEHLAR
NPFGKVPVLEDGDLTLFESRAIARHVLRKHKPELLGGGRLEQTAMVDVWL
EVEAHQLSPPAIAIVVECVFAPFLGRERNQAVVDENVEKLKKVLEVYEAR
LATCTYLAGDFLSLADLSPFTIMHCLMATEYAALVHALPHVSAWWQGLAA
RPAANKVAQFMPVGAGAPKEQE
>GTH1_MAIZE
APMKLYGAVMSWNLTRCATALEEAGSDYEIVPINFATAEHKSPEHLVRNP
FGQVPALQDGDLYLFESRAICKYAARKNKPELLREGNLEEAAMVDVWIEV
EANQYTAALNPILFQVLISPMLGGTTDQKVVDENLEKLKKVLEVYEARLT
KCKYLAGDFLSLADLNHVSVTLCLFATPYASVLDAYPHVKAWWSGLMERP
SVQKVAALMKPSA
>GTH1_WHEAT
MSPVKVFGHPMLTNVARVLLFLEEVGAEYELVPMDFVAGEHKRPQHVQLN
PFAKMPGFQDGDLVLFESRAIAKYILRKYGGTAGLDLLGENSGIEELAMV
DVWTEVEAQQYYPAISPVVFECIIIPFIIPGGGAAPNQTVVDESLERLRG
VLGIYEARLEKSRYLAGDSITFADLNHIPFTFYFMTTPYAKVFDDYPKVK
AWWEMLMARPAVQRVCKHMPTEFKLGAQY
>GTH5_ARATH
MVTVKLYGMAYSTCTKRVYTTAKEIGVDVKIVPVDLMKGEHKEPAYLDNY
HPFGVIPVLEDEDGTKIYESRAISRYLVAKYGKGSSLLPSPSDPKAYGLF
EQAASVEYSSFDPPASSLAYERVFAGMRGLKTNEELAKKYVDTLNAKMDG
YERILSKQKYLAGNDFTLADLFHLPYGAMVAQLEPTVLDSKPHVKAWWAA
SLRVIPGRLLRNSSKEFM
>1eem_A
SARSLGKGSAPPGPVPEGSIRIYSMRFCPFAERTRLVLKAKGIRHEVINI
NLKNKPEWFFKKNPFGLVPVLENSQGQLIYESAITCEYLDEAYPGKKLLP
DDPYEKACQKMILELFSKVPSLVGSFIRSQNKEDYAGLKEEFRKEFTKLE
EVLTNKKTTFFGGNSISMIDYLIWPWFERLEAMKLNECVDHTPKLKLWMA
AMKEDPTVSALLTSEKDWQGFLELYLQNSPEACDYGL
>GTO1_MOUSE
MSGESSRSLGKGSAPPGPVPEGQIRVYSMRFCPFAQRTLMVLKAKGIRHE
VININLKNKPEWFFEKNPLGLVPVLENSQGHLVTESVITCEYLDEAYPEK
KLFPDDPYKKARQKMTLESFSKVPPLIASFVRSKRKEDSPNLREALENEF
KKLEEGMDNYKSFLGGDSPSMVDYLTWPWFQRLEALELKECLAHTPKLKL
WMAAMQQDPVASSHKIDAKTYREYLNLYLQDSPEACDYGL
>GTO2_HUMAN
MSGDATRTLGKGSQPPGPVPEGLIRIYSMRFCPYSHRTRLVLKAKDIRHE
VVNINLRNKPEWYYTKHPFGHIPVLETSQCQLIYESVIACEYLDDAYPGR
KLFPYDPYERARQKMLLELFCKVPHLTKECLVALRCGRECTNLKAALRQE
FSNLEEILEYQNTTFFGGTCISMIDYLLWPWFERLDVYGILDCVSHTPAL
RLWISAMKWDPTVCALLMDKSIFQGFLNLYFQNNPNAFDFGLC
>YKJ3_CAEEL
MTVLAGVNSKIVKNGCWNHSYLQHAILPVAQRALIYASVKNIPSDVINVH
LQEKPDWYFSKHYKGQVPTLEHDEGKKHVIESAVIPEYLDDIYPETRILP
TDPYEKVQQKLLLDRISGQVSPAFYGVVQAVKNPDLREEKFADIKKAYDN
AEQLLTGDFYSGTSKPGFVDYLLYPNIQRAYWAAHIVPDFPLEAESFPGP
NYPRLSKWYKALESIPEVAAASQPTENGVGFFKDYLGGSPNYDYGLTKLS
ETI
kalign-3.3.1/dev/data/README 0000664 0000000 0000000 00000000312 14036164772 0015340 0 ustar 00root root 0000000 0000000 This directory contains test alignments:
- distributed together with Sean Eddy's easel library: https://github.com/EddyRivasLab/easel
- from the balibase MSA benchmark: https://www.lbgi.fr/balibase/
kalign-3.3.1/dev/data/README~ 0000664 0000000 0000000 00000000207 14036164772 0015541 0 ustar 00root root 0000000 0000000 This directory contains test alignment files distributed together with Sean Eddy's easel library: https://github.com/EddyRivasLab/easel kalign-3.3.1/dev/data/a2m.good.1 0000664 0000000 0000000 00000001252 14036164772 0016154 0 ustar 00root root 0000000 0000000 >MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA
pivdtgsvApLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDtekMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVI---------ADTVAAGDAGFEKLMSMICILLRSAY-------
>HBB_HUMAN
VhLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNP
KVKAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHF
GKEFTPPVQAAYQKVVAGVANALAHKYH------
>HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF------DLSHGSAQ
VKGHGKKVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLP
AEFTPAVHASLDKFLASVSTVLTSKYR------
kalign-3.3.1/dev/data/a2m.good.2 0000664 0000000 0000000 00000000631 14036164772 0016155 0 ustar 00root root 0000000 0000000 >tRNA2
UCCGAUAUAGUGUAACGGCUAUCACAUCACGCUUUCACCGUGGAGACCGGGGUUCGACUC
CCCGUAUCGGAG
>tRNA3
UCCGUGAUAGUUUAAUGGUCAGAAUGG-GCGCUUGUCGCGUGCcAGAUCGGGGUUCAAUU
CCCCGUCGCGGAG
>tRNA5
GGGCACAUGGCGCAGUUGGUAGCGCGCUUCCCUUGCAAGGAAGaGGUCAUCGGUUCGAUU
CCGGUUGCGUCCA
>tRNA1
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGaGGUCCUGUGUUCGAUC
CACAGAAUUCGCA
>tRNA4
GCUCGUAUGGCGCAGUGG-UAGCGCAGCAGAUUGCAAAUCUGUuGGUCCUUAGUUCGAUC
CUGAGUGCGAGCU
kalign-3.3.1/dev/data/afa.good.1 0000664 0000000 0000000 00000001315 14036164772 0016224 0 ustar 00root root 0000000 0000000 >MYG_PHYCA
--------V-LSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
EAEMKASEDLKKHGVTVLTALGAILKKKGH---HEAELKPLAQSHATKHKIPIKYLEFIS
EAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVI---------ADTVAAGDAGFEKLMSMICILLRSAY-------
>HBB_HUMAN
--------VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
PDAVMGNPKVKAHGKKVLGAFSDGLAHLDN---LKGTFATLSELHCDKLHVDPENFRLLG
NVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
>HBA_HUMAN
--------V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-----
-DLSHGSAQVKGHGKKVADALTNAVAHVDD---MPNALSALSDLHAHKLRVDPVNFKLLS
HCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
kalign-3.3.1/dev/data/afa.good.2 0000664 0000000 0000000 00000000632 14036164772 0016226 0 ustar 00root root 0000000 0000000 >tRNA2
UCCGAUAUAGUGUAACGGCUAUCACAUCACGCUUUCACCGUGG-AGACCGGGGUUCGACU
CCCCGUAUCGGAG
>tRNA3
UCCGUGAUAGUUUAAUGGUCAGAAUGG-GCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUU
CCCCGUCGCGGAG
>tRNA5
GGGCACAUGGCGCAGUUGGUAGCGCGCUUCCCUUGCAAGGAAGAGGUCAUCGGUUCGAUU
CCGGUUGCGUCCA
>tRNA1
GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC
CACAGAAUUCGCA
>tRNA4
GCUCGUAUGGCGCAGUGG-UAGCGCAGCAGAUUGCAAAUCUGUUGGUCCUUAGUUCGAUC
CUGAGUGCGAGCU
kalign-3.3.1/dev/data/afa.good.3 0000664 0000000 0000000 00000001615 14036164772 0016231 0 ustar 00root root 0000000 0000000 >7295730___KOG0003
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrilaqkyncdkmicrkcy
arlhpratncrkkkcghtnnlrpkkklk
>Hs4507761___KOG0003
mqifvktltgktitlevepsdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrqlaqkyncdkmicrkcy
arlhpravncrkkkcghtnnlrpkkkvk
>At3g52590___KOG0003
mqifvktltgktitlevessdtidnvkakiqdkegippdqqrlifagkql
edgrtladyniqkestlhlvlrlrggiiepslmmlarkynqdkmicrkcy
arlhpravncrkkkcghsnqlrpkkkik
>CE15495___KOG0003
mqifvktltgktitleveasdtienvkakiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslrqlaqkyncdkqicrkcy
arlpprasncrkkkcghsselrikkklk
>SPAC1805.12c___KOG0003
mqifvktltgktitlevessdtidnvkskiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslkalaskyncekqicrkcy
arlppratncrkkkcghtnqlrpkkklk
>YIL148w___KOG0003
mqifvktltgktitlevessdtidnvkskiqdkegippdqqrlifagkql
edgrtlsdyniqkestlhlvlrlrggiiepslkalaskyncdksvcrkcy
arlppratncrkrkcghtnqlrpkkklk
kalign-3.3.1/dev/data/clustal.good.1 0000664 0000000 0000000 00000002145 14036164772 0017146 0 ustar 00root root 0000000 0000000 MUSCLE (3.7) multiple sequence alignment
MYG_PHYCA --------V-LSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKT
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
HBB_HUMAN --------VHLTPEEKSAVTALWGKV--NVDEVGGEALGRLLVVYPWTQRFFESFGDLST
HBA_HUMAN --------V-LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF-----
. *: :. : *. * * : * .:: * : * *
MYG_PHYCA EAEMKASEDLKKHGVTVLTALGAILKKKGH---HEAELKPLAQSHATKHKIPIKYLEFIS
GLB5_PETMA ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
HBB_HUMAN PDAVMGNPKVKAHGKKVLGAFSDGLAHLDN---LKGTFATLSELHCDKLHVDPENFRLLG
HBA_HUMAN -DLSHGSAQVKGHGKKVADALTNAVAHVDD---MPNALSALSDLHAHKLRVDPVNFKLLS
. .:. *. : *. : . : *: *. . .: : .:.
MYG_PHYCA EAIIHVLHSRHPGDFGADAQGAMNKALELFRKDIAAKYKELGYQG
GLB5_PETMA AVI---------ADTVAAGDAGFEKLMSMICILLRSAY-------
HBB_HUMAN NVLVCVLAHHFGKEFTPPVQAAYQKVVAGVANALAHKYH------
HBA_HUMAN HCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSKYR------
: : . .. :* : . : *
kalign-3.3.1/dev/data/clustal.good.2 0000664 0000000 0000000 00000001261 14036164772 0017145 0 ustar 00root root 0000000 0000000 CLUSTAL W (1.81) multiple sequence alignment
tRNA2 UCCGAUAUAGUGUAACGGCUAUCACAUCACGCUUUCACCGUGG-AGACCGGGGUUCGACU
tRNA3 UCCGUGAUAGUUUAAUGGUCAGAAUGG-GCGCUUGUCGCGUGCCAGAUCGGGGUUCAAUU
tRNA5 GGGCACAUGGCGCAGUUGGUAGCGCGCUUCCCUUGCAAGGAAGAGGUCAUCGGUUCGAUU
tRNA1 GCGGAUUUAGCUCAGUUGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC
tRNA4 GCUCGUAUGGCGCAGUGG-UAGCGCAGCAGAUUGCAAAUCUGUUGGUCCUUAGUUCGAUC
* * * * * * * **** *
tRNA2 CCCCGUAUCGGAG
tRNA3 CCCCGUCGCGGAG
tRNA5 CCGGUUGCGUCCA
tRNA1 CACAGAAUUCGCA
tRNA4 CUGAGUGCGAGCU
*
kalign-3.3.1/dev/run_aln_test.sh 0000775 0000000 0000000 00000001041 14036164772 0016603 0 ustar 00root root 0000000 0000000 #!/usr/bin/env bash
echo "Running kalign basic alignment tests:";
testfiles=("BB11001.msf" "BB11001_EOF.msf" "BB11001.tfa" "BB12006.msf" "BB12006.tfa" "BB30014.msf" "BB30014.tfa")
for i in "${testfiles[@]}"
do
echo $i
error=$( ../src/kalign --devtest $i -o test.afa 2>&1 )
status=$?
if [[ $status -eq 0 ]]; then
printf "%10s%10s%10s\n" read/write $i SUCCESS;
else
printf "%10s%10s%10s\n" read/write $i FAILED;
printf "with ERROR $status and Message:\n\n$error\n\n";
exit 1;
fi
done
kalign-3.3.1/dev/run_io_test.sh 0000775 0000000 0000000 00000001001 14036164772 0016434 0 ustar 00root root 0000000 0000000 #!/usr/bin/env bash
echo "Running kalign basic io test:";
testfiles=("a2m.good.1" "a2m.good.2" "afa.good.1" "afa.good.2" "afa.good.3" "clustal.good.1" "clustal.good.2")
for i in "${testfiles[@]}"
do
echo $i
error=$( ../src/rwaln $i 2>&1 )
status=$?
if [[ $status -eq 0 ]]; then
printf "%10s%10s%10s\n" read/write $i SUCCESS;
else
printf "%10s%10s%10s\n" read/write $i FAILED;
printf "with ERROR $status and Message:\n\n$error\n\n";
exit 1;
fi
done
kalign-3.3.1/doc/ 0000775 0000000 0000000 00000000000 14036164772 0013542 5 ustar 00root root 0000000 0000000 kalign-3.3.1/doc/images/ 0000775 0000000 0000000 00000000000 14036164772 0015007 5 ustar 00root root 0000000 0000000 kalign-3.3.1/doc/images/Balibase_scores.jpeg 0000664 0000000 0000000 00000520003 14036164772 0020736 0 ustar 00root root 0000000 0000000 ˙Ø˙ā JFIF ,, ˙Û C
$.' ",#(7),01444'9=82<.342˙Û C
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