NAME

       prank - Computes probabilistic multiple sequence alignments

SYNOPSIS

       prank sequence_file

       prank [optional parameters] -d=sequence_file [optional parameters]

DESCRIPTION

       The Probabilistic Alignment Kit (PRANK) is a probabilistic multiple alignment program for
       DNA, codon and amino-acid sequences. It's based on a novel algorithm that treats
       insertions correctly and avoids over-estimation of the number of deletion events.

       In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and
       correctly takes into account the evolutionary distances between sequences. Lastly, PRANK
       allows for defining a potential structure for sequences to be aligned and then,
       simultaneously with the alignment, predicts the locations of structural units in the
       sequences.

OPTIONS

   INPUT/OUTPUT PARAMETERS
       -d=sequence_file
               The input sequence file in FASTA format.

       -t=tree_file
               The tree file to use. If unset, an appriximated NJ tree is generated.

       -o=output_file
               Set the name of the output file. If unset, output_file is set to output.

       -f=output_format
               Set the output format. output_format can be one of fasta (default), phylipi,
               phylips, paml, or nexus.

       -m=model_file
               The model file to use. If unset, model_file is set to HKY2/WAG.

       -support
               Compute posterior support.

       -showxml
               Output alignment xml-file.

       -showtree
               Output alignment guidetree.

       -showanc
               Output ancestral sequences.

       -showall
               Output all of these.

       -noanchors
               Do not use Exonerate anchoring. (Exonerate to be installed separately.)

       -nomafft
               Do not use MAFFT for guide tree. (MAFFT to be installed separately.)

       -njtree Estimate tree from an input alignment (and realign).

       -shortnames
               Truncate names at first space character.

       -quiet  Reduce output.

   ALIGNMENT MERGE
       -d1=alignment_file
               The first input alignment file in FASTA format.

       -d2=alignment_file
               The second input alignment file in FASTA format.

       -t1=tree_file
               The tree file for the first alignment. If unset, an appriximated NJ tree is
               generated.

       -t2=tree_file
               The tree file for the second alignment. If unset, an appriximated NJ tree is
               generated.

   MODEL PARAMETERS
       -F, +F  Force insertions to be always skipped.

       -gaprate=#
               Set the gap opening rate. The default is 0.025 for DNA and 0.005 for proteins.

       -gapext=#
               Set the gap extension probability. The default is 0.75 for DNA and 0.5 for
               proteins.

       -codon  Use empirical codon model for coding DNA.

       -DNA, -protein
               Use DNA or protein model, respectively. Disables auto-detection of model.

       -termgap
               Penalise terminal gaps normally.

       -nomissing
               No missing data. Use -F for terminal gaps.

       -keep   Do not remove gaps from pre-aligned sequences.

   OTHER PARAMETERS
       -iterate=#
               Rounds of re-alignment iteration; by default, iterate five times and keep the best
               result.

       -once   Run only once. Same as -iterate=1.

       -prunetree
               Prune guide tree branches with no sequence data.

       -prunedata
               Prune sequence data with no guide tree leaves.

       -uselogs
               Slower but should work for a greater number of sequences.

       -translate
               Translate input data to protein sequences.

       -mttranslate
               Translate input data to protein sequencess using mt table.

       -convert
               Do not align, just convert to a different format.

       -dna=dna_sequence_file
               DNA sequence file for backtranslation of protein alignment.

       -help   Show an extended help page with more options.

       -version
               Show version and check for updates.

AUTHORS

       prank was written by Ari Loytynoja.

       This manual page was originally written by Manuel Prinz <manuel@debian.org> for the Debian
       project (and may be used by others).