Output options:¶

-o <file>

HMM file to be written to (default=<infile.hhm>)

-a <file>

HMM file to be appended to

-v <int>

verbose mode: 0:no screen output 1:only warings 2: verbose

-seq <int>

max. number of query/template sequences displayed (def=10) Beware of overflows! All these sequences are stored in memory.

-add_cons

make consensus sequence master sequence of query MSA

-name <name>

use this name for HMM (default: use name of first sequence)

Filter query multiple sequence alignment

-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=100)

-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

Pseudocount (pc) options:¶

Context specific hhm pseudocounts:

-pc_hhm_contxt_mode {0,..,3}

position dependence of pc admixture 'tau' (pc mode, default=0)

0: no pseudo counts:

tau = 0

1: constant

tau = a

2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c) 3: CSBlast admixture: tau = a(1+b)/(Neff[i]+b) (Neff[i]: number of effective seqs in local MSA around column i)

-pc_hhm_contxt_a

[0,1] overall pseudocount admixture (def=0.9)

-pc_hhm_contxt_b

[1,inf[ Neff threshold value for mode 2 (def=4.0)

-pc_hhm_contxt_c

[0,3] extinction exponent c for mode 2 (def=1.0)

Context independent hhm pseudocounts (used for templates; used for query if contxt file is not available):

-pc_hhm_nocontxt_mode {0,..,3}

position dependence of pc admixture 'tau' (pc mode, default=2)

0: no pseudo counts:

tau = 0

1: constant

tau = a

2: diversity-dependent: tau = a/(1+((Neff[i]-1)/b)^c) (Neff[i]: number of effective seqs in local MSA around column i)

-pc_hhm_nocontxt_a

[0,1] overall pseudocount admixture (def=1.0)

-pc_hhm_nocontxt_b

[1,inf[ Neff threshold value for mode 2 (def=1.5)

-pc_hhm_nocontxt_c

[0,3] extinction exponent c for mode 2 (def=1.0)

Context-specific pseudo-counts:

-nocontxt

use substitution-matrix instead of context-specific pseudocounts

-contxt <file> context file for computing context-specific pseudocounts (default=./data/context_data.crf)

Other options:¶

-maxres <int>

max number of HMM columns (def=20001)

Example: hhmake -i test.a3m