BIGtigr

80_genomes

code for analyzing loss and gain of a gene among many genomes

coalescent-theory

NOT FREE SOFTWARE UNTIL AFTER MAY

finalseg

Chinese Words Segment Library based on HMM model

GenomeAlign

HMM

隐马尔科夫模型进行中文分词 python

Scripts

BioExt

A few handy bioinformatics tools not already within BioPython

Bioinformatics-1

Homework 3

genblastA_to_gff

haemonchus-comparison

Code used for comparison of two Haemonchus contortus genomes, in my honours thesis at the University of Calgary.

HeteroScan

A Tool to identify and quantify Heterozygosity in Genome

HMM-and-Bayesian-HMM

Dicrete and Mixture of Gaussian HMM and Bayesian HMM(离散和混合高斯隐马尔可夫模型和贝叶斯隐马尔可夫模型)

HMM-python

用python实现了隐马尔科夫模型的概率计算和预测部分，主要是前向后向算法和维特比算法

kingman

An example Python package, which simulates Kingman's coalescent.

MCMCPYJW

various MCMC and apadive MCMC script

mle-for-nowcasting

Example of maximum likelihood estimation in Python (follows Matlab code)

np-hmm

General Bayesian non-parametric hidden Markov model

PAMLpipeline

Shell scripts for running batch PAML

PhosCalc

The Sainsbury Lab Tool for estimating the likelihood of phosphorylation at possible sites in a peptide from Mass Spec data

plinkline

Finding regions of selection with iHS and XP-EHH, a pipeline between PLINK, scripts from the Pritchard lab and beyond.

Primer_Scientific_Programming

Files for A Primer on Scientific Programming with Python (4th) by H.P. Langtangen

python-biplot

Generates simple biplot using common scientific Python packages

PythonHMM

A toy Python implementation of the Hidden Markov Model.

reciprocal_smallest_distance

Reciprocal Smallest Distance (RSD) is a pairwise orthology algorithm that uses global sequence alignment and maximum likelihood evolutionary distance between sequences to accurately detects orthologs between genomes.

Silva2014_RustPhylogenomics

The set of scripts used in Silva et al. 2014 "Genomic patterns of positive selection at the origin of rust fungi"

Speech_Recognition

A simple speech recognition using HMM (python)

SWAMP

Sliding Window Alignment Masker for PAML

Traveling-Salesman-MCMC-approach

Markov Chain Monte Carlo (MCMC) practice

xgcode

A server for a collection of web-accessible python scripts.