How to use phyloHMM?

Quick start

Required parameter

–ali (input alignment)

–output_path (path)

the directory of your output path

Optional parameter

–mode con(default)|rep

how to construct a sequence for HMM data base search + con : generate a consensus sequence found using hmmemit --symfrac 0 + rep : pick up a representative single sequence from input alignment with highest pairwise similarity

–database (hmm database)

the hmm database you want to use. (default version: 3.1b1 | May 2013)

–file_name (output file name)

your output file name. (default is your input file name)

–hmmer_path (path)

the path of your hmmer scripts (hmmfetch hmmpress hmmscan) (default version: h3.1b2 | February 2015)

–gb_path (path)

the path of your gblocks file (default version: 0.91b) #### –iq_path (path) the path of your iqtree file (default version: 1.6.10)

Example

use command:

python3 freq_extractor.py –ali example_files/example_input.fasta –output_path output –file_name example1 ## Support or Contact

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