mf2q,sbotond

mf2q's Introduction

mf2q

mf2q is a Python script calculating Q matrices scaled to give one expected substitution per unit time from mutation count data using the DCFreq method.

Issue make to run tests using input files under t.

Reference

Kosiol C., Goldman N. (2005) Different versions of the Dayhoff rate matrix. Mol Biol Evol 22:193-199 doi:10.1093/molbev/msi005

Usage

usage: mf2q [-h] [-f freq_file] [-o out_file] [-t tolm] [-s] [input file]

Produce scaled Q matrices from mutation counts using the DCFreq method
(version 1.0).

positional arguments:
  input file    Mutation counts in a tab separated format(row=from, column=to,
                see examples).

optional arguments:
  -h, --help    show this help message and exit
  -f freq_file  Symbol frequency file.
  -o out_file   Output file
  -t tolm       Tolerance multiplier. Increase it if equilibrium distribution
                cannot be recovered.
  -s            Do not scale the Q matrix (default: False).

Example input

    T   C   A   G
T   171 293 229 306
C   73  390 229 306
A   38  153 355 453
G   38  153 339 468

Example output

# Symbols:
T       C       A       G

# Equilibrium distribution:
5.242828e-02    2.106127e-01    3.156225e-01    4.213365e-01

# Q matrix:
-1.383726e+00   4.896518e-01    3.826971e-01    5.113769e-01
1.221174e-01    -1.017087e+00   3.830806e-01    5.118893e-01
6.350432e-02    2.556885e-01    -1.076231e+00   7.570384e-01
6.356796e-02    2.559447e-01    5.670931e-01    -8.866057e-01