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Google core libraries for Java

Modern Java - A Guide to Java 8

A new data structure for accurate on-line accumulation of rank-based statistics such as quantiles and trimmed means

Command line parsing framework for Java

Official code repository for GATK versions 4 and up

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

Bayesian Evolutionary Analysis Sampling Trees

The stairway plot is a method for inferring detailed population demographic history using the site frequency spectrum (SFS) from DNA sequence data.

The SPrime program identifies variants that are introgressed from archaic populations.

A coalsecent simulator with selection

SimRA (Simulation based on Random-graphs Algorithms) is a framework for simulating generic and complex evolutionary scenarios of multiple populations with subdivision and admixture. The algorithm g…

JAVA source code to implement the ABC-DL approach described in Mondal et al

diCal2 infers complex demographic histories from whole-genome sequencing data

repository for code and releases of PIQMEE add-on for BEAST2