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 <[email protected]> for the Debian project (and may be used by others).