hmm2aln.pl

script to automate gene family phylogeny based using HMM

REQUIREMENTS

HMMER http://hmmer.org/download.html
JFR::Fasta https://github.com/josephryan/JFR-PerlModules

INSTALL

   git clone https://github.com/josephryan/hmm2aln.pl
   cd hmm2aln.pl

To install these modules and scripts type the following:

   perl Makefile.PL
   make
   sudo make install

To install without root privelages try:

   perl Makefile.PL PREFIX=/home/myuser/scripts
   make
   make install

Or just copy scripts to a directory and run them like this:

   perl hmm2aln.pl

hmm2aln.pl

script takes an HMM and a multi-sequence FASTA file (or directory of FASTA files) and produces an alignment.

SYNOPSIS

hmm2aln.pl --hmm= --name= {--fasta=|--fasta_dir=<fasta_dir>} [--threads=] [--no_clean] [--nofillcnf=<nofill.conf>] [--help] [--version]

OPTIONS

   --hmm
        hmmfile (e.g. download http://pfam.xfam.org/family/PF00096/hmm)

   --name
        name used for output files

   --fasta
        FASTA-formatted file with multiple sequences

   --fasta_dir
        directory with FASTA-formatted files

   --threads
        number of threads to use for search

   --no_clean
        do not remove intermediate files created by hmmer

   --nofillcnf
        HMMer can make alignments from an hmmsearch but often misses the ends of alignments. hmm2aln.pl rescues these missing bits, and uses the --nofillcnf option (see nofill.hox.conf file) to make sure it doesn't rescue garbage.  The option requires that certain residue positions only be rescued if they are certain amino acids. See example file (https://github.com/josephryan/hmm2aln.pl/blob/master/nofill.hox.conf) for format.

   --help
        print this manual

   --version
        print the version. Overrides all other options.

stockholm2fasta.pl

script used by hmm2aln.pl to convert Stockholm-formatted multiple sequence alignment to FASTA-formatted sequence alignment. Uses esl-reformat program, which comes with HMMer, but since esl-reformat will not print fasta with gaps this script uses esl-reformat to print a fasta (long deflines) and phys format (short deflines but seqs w/gaps) and then prints a hybrid of the 2 (long defs and seqs w/gaps)

BUGS Please report them to Joseph Ryan joseph.ryan@whitney.ufl.edu

This program 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 <http://www.gnu.org/licenses/>.