hillerlab

TOGA

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

GenomeAlignmentTools

Tools for improving the sensitivity and specificity of genome alignments

make_lastz_chains

Portable solution to generate genome alignment chains using lastz

CESAR2.0

GeneLossPipe

ForwardGenomics

Methods for finding associations between phenotypic and genomic differences between species using the Forward Genomics framework

IterativeErrorCorrection

Iterative error correction of long reads

REforge

Regulatory Element Forward Genomics to associate transcription factor binding site divergence in regulatory elements with phenotypic differences between species

CESAR

Coding Exon Structure Aware Realigner

Parasol_LSF_Slurm

A parasol-like wrapper around LSF or Slurm for efficiently handling batches of jobs on a compute cluster

TFforge

Identifying transcription factors involved in phenotypic differences between species