phyloHMM (now this is underconstruction)

per-site amino-acid frequency profiles of protein domains. A detailed document is avaiable in the readthedocs of phyloHMM

Usage

1. Clone the repo.
2. Go to the project's root folder.
3. Please install python and biopython.
4. Use python to execuate your files.

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 hmmbuild hmmemit) (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

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