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Trinity RNA-Seq de novo transcriptome assembly
Automatically exported from code.google.com/p/cdhit
A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data
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
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
GALBA is a pipeline for fully automated prediction of protein coding gene structures with AUGUSTUS in novel eukaryotic genomes for the scenario where high quality proteins from one or several close…
Dfam Transposable Element Tools Docker container.
An accurate and ultra-fast hybrid genome assembler
Mapping pipeline for data generated using Arima-HiC
Scripts to estimate genome size and coverage from kmer distribution generated by jellyfish
The Ensembl Compara Perl API and SQL schema
use long sequenced reads to close gaps in assemblies
FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. Th…
Dinoflagellate Annotation Workflow
TreeGrafter is a new software tool for annotating uncharacterized protein sequences, using annotated phylogenetic trees.
identify potential non-animal transcripts in animal transcriptomes
Program to run the SOWH test (likelihood-based test used to compare tree topologies which are not specified a priori)
use paired-end transcriptome reads to scaffold genomes
BOSTIn is a new, user-friendly phylogenetic artifact identification package.
Feature-aware orthology prediction tool. Provided data package: Quest for Orthologs reference gene sets 2019.
APP is a phyletic pattern analysis tool that uses comparative genomics to detect horizontally acquired genes.