This is the command prank that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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 <[email protected]> for the Debian
project (and may be used by others).
Use prank online using onworks.net services
