prank - Computes probabilistic multiple sequence alignments
prank sequence_file
prank [optional parameters] -d=sequence_file
[optional parameters]
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.
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.
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).