This is the command hhfilter 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
hhfilter - filter an alignment by maximum sequence identity of match states and minimum
coverage
SYNOPSIS
hhfilter -i infile -o outfile [options]
DESCRIPTION
HHfilter version 2.0.16 (January 2013) Filter an alignment by maximum sequence identity of
match states and minimum coverage (C) Johannes Soeding, Michael Remmert, Andreas Biegert,
Andreas Hauser Remmert M, Biegert A, Hauser A, and Soding J. HHblits: Lightning-fast
iterative protein sequence searching by HMM-HMM alignment. Nat. Methods 9:173-175 (2011).
-i <file>
read input file in A3M/A2M or FASTA format
-o <file>
write to output file in A3M format
-a <file>
append to output file in A3M format
OPTIONS
-v <int>
verbose mode: 0:no screen output 1:only warings 2: verbose
-id [0,100] maximum pairwise sequence identity (%) (def=90)
-diff [0,inf[
filter MSA by selecting most diverse set of sequences, keeping at least this many
seqs in each MSA block of length 50 (def=0)
-cov [0,100] minimum coverage with query (%) (def=0)
-qid [0,100] minimum sequence identity with query (%) (def=0)
-qsc [0,100] minimum score per column with query (def=-20.0)
-neff [1,inf]
target diversity of alignment (default=off)
Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert; '-' = Delete; '.' =
gaps aligned to inserts (may be omitted)
-M first
use FASTA: columns with residue in 1st sequence are match states
-M [0,100]
use FASTA: columns with fewer than X% gaps are match states
Example: hhfilter -id 50 -i d1mvfd_.a2m -o d1mvfd_.fil.a2m
Use hhfilter online using onworks.net services
