PSMC

1 Overview | 2 Using | 2.1 Example

Overview

The Pairwise Sequentially Markovian Coalescent (PSMC) method uses the genome sequence of a single individual to estimate demographic history covering a time span of thousands of generations.

Using

Use the module name psmc to discover versions available and to load the application.

Example

[]$ psmc Program: psmc (Pairwise SMC Model) Version: 0.6.5-r67 Contact: <http://hengli.uservoice.com/> Usage: psmc [options] input.txt Options: -p STR pattern of parameters [4+5*3+4] -t FLOAT maximum 2N0 coalescent time [15] -N INT maximum number of iterations [30] -r FLOAT initial theta/rho ratio [4] -c FILE CpG counts generated by cntcpg [null] -o FILE output file [stdout] -i FILE input parameter file [null] -T FLOAT initial divergence time; -1 to disable [-1] -b bootstrap (input be preprocessed with split_psmcfa) -S simulate sequence -d perform decoding -D print full posterior probabilities []$ calD Usage: calD [options] <U.fa> <V.fa> <X.fa> <Y.fa> Options: -w INT window size for block Jack-Knife [1000000] -q INT quality threshold [0] -M FILE mask regions in BED FILE [null] -s INT step size (effective with -b) [100] -b binary output []$ cntcpg Usage: cntcpg [-b] [-s 100] [-n 0.9] <in.fa> Output: 5 numbers: #CpG #CpG-ts #nonCpG #nonCpG-ts+tv #tv []$ fq2psmcfa Usage: fq2psmcfa [-cnvx] [-q 10] [-g 10000] [-s 100] <in.fq> []$ mutDiff Usage: mutDiff [-bl] [-s 100] <1.fa> <2.fa> <outgroup.fa> []$ splitfa Usage: splitfa <in.fa> [trunk_size=500000]