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accumulate

code for calling mutatons from MA lines

add-to-qiime-db

Small set of scripts to ease the expansion of a Qiime reference database

bamtools

C++ API & command-line toolkit for working with BAM data

bioinfo

Various bioinformatics tools

braker

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes

branchrates

Calculates branch-specific evolutionary rates for homologous characters

bx-python

Tools for manipulating biological data, particularly multiple sequence alignments

chrom-gc

Models chromosome structure to study recombination

compleasm

A genome completeness evaluation tool based on miniprot

data

Data repository, containing published and unpublished datasets

dates

Method for dating admixture in ancient DNA specimens

dispersaldiversity

Analyse individual and genetic diversity of dispersal processes in biological populations

dispr

Degenerate In-Silico PcR

ebc-perl-hacks

Repository for the Perl Hacks meeting group in the Evolutionary Biology Centre at Uppsala University

eigensoft

Uppmax-specific fork of https://www.hsph.harvard.edu/alkes-price/software/

fastrank

R package providing fast ranking for integer and numeric vectors, an alternative to calling .Internal(rank(...))

frc_align

Computes FRC from SAM/BAM file and not from afg files

gameteutils

Set of tools for analysing the genetics and genomics of gametes

garli

Automatically exported from code.google.com/p/garli

geneticsimlib

Update of John Conery's Genetic Simulation Library

hcluster

My git clone of Heng Li's hcluster from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/

hpf

Convert HPF data from QuickDAQ monitoring machine to TXT or CSV, because files that are too large cannot be converted with the software provided with the machine.

irys-scaffolding

scripts to parse IrysView output

jmers

Kmer-guided processing of jumping reads

k

K implements Kondrashov's 1985 model for genomic mutation, with some extras

latentstrainanalysis

Partitioning and analysis methods for large, complex sequence datasets

mlgtest

Implements a conservative test for asexuality based on the number of observed multilocus genotypes

nestedrankstest

R package providing a mixed-model Mann-Whitney-Wilcoxon test with nested ranks

orthomcl

pacbio-utilities

Collection of utilities for working with PacBio-based assemblies