BIGtigr

convCal

Python scripts for calculation of expected number of convergence in Zou and Zhang 2015

Coursera-Bioinformatics

My solution to Bioinformatics Specialization (Finding Hidden Messages in DNA; Genome Sequencing; Comparing Genes, Proteins, and Genomes; Molecular Evolution; Genomic Data Science and Clustering; Finding Mutations in DNA and Proteins; Bioinformatics Capstone: Big Data in Biology)

Dot2dot

Dot2dot: Accurate Whole-Genome Tandem Repeats Discovery

go_enrichment

Transcripts annotation and GO enrichment Fisher tests

MCMC

Collection of Monte Carlo (MC) and Markov Chain Monte Carlo (MCMC) algorithms applied on simple examples.

augustus2

BamDeal

BamDeal: a comprehensive toolkit for bam manipulation

bhmm

Bayesian hidden Markov models toolkit

bioinformatics-2

Assignments of Bioinformatics Lab

BSseeker2

A versatile aligning pipeline for bisulfite sequencing data

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

ClustCompare

Pipeline to compare secondary metabolite biosynthetic gene clusters (BGCs)

coalescent-trees

Simulates coalescent trees, DNA sequences within it, reconstructing them and inferring a posterior distribution of the effective population size.

codeml

Machine learning trainigs and code

convergentEvolution-1.0

DeOldify

A Deep Learning based project for colorizing and restoring old images

dnds

Calculate dN/dS ratio precisely (Ka/Ks) using a codon-by-codon counting method.

ensembl-pipeline

Job management for the Ensembl Genebuild pipeline

funannotate

Eukaryotic Genome Annotation Pipeline

genome_analysis

grand-conv

Rapid, interactive, probabilistic analysis of convergent molecular evolution

maf2synteny

A tool for recovering synteny blocks from multiple alignment

msmc

Implementation of the multiple sequential markovian coalescent

NCBI_contamination_fix

ngs-1

Next Generation Shell (NGS)

Pfam

Pfam codebase

practicalAI

A practical approach to learning machine learning.

treetime_examples

A collection of documented examples using TreeTime

tripal_go

go enrichment for tripal

xpclr

Code to compute the XP-CLR statistic to infer natural selection