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egas

DEPRECATED: Whole genome self alignments procedure for finding segment duplications (and partial WGD).

egaz

(DEPRECATED) The backend of Easy Genome Aligner

faops

faops operates fasta files

fars

Command line tools for fasta files

fig_table

Create figs and tables from excel files. Mainly works on Windows.

gars

Genome Analyst with Rust and Redis

gawm

(DEPRECATED) GAWM - Genome Analyst with Mongodb

genomes

homebrew-tap

My tap for unbrewed repos

intspan

Command line tools for IntSpan related bioinformatics operations

jvarkit

Java utilities for Bioinformatics

lecture-slides

Slides for my course "General Biology".

miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)

mtheme

A modern LaTeX Beamer theme

multiz

A strip-down version of multiz-tba

newicktree

Draw Newick format phylogenetic trees.

nwr

`nwr` is a command line tool for working with NCBI taxonomy, Newick files and assembly reports

one-liners

Useful bash one-liners

pars

Processing Yeast PARS Data

phylo-tree

Create phylogenetics trees by xelatex/tikz/forest

plastid

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

rw

Resize windows on macOS/Windows

scythe

A 3'-end adapter contaminant trimmer

simulation

Some population genetic simulations

sparsemem

http://compbio.cs.princeton.edu/mems/

sra

Work with NCBI SRA/EBI ENA

task-ega

Task::EGA - EGA bundle

tool

DEPRECATED: tools of my own.

ubuntu

Setting-up scripts for Ubuntu 20.04