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ab12phylo

AB12PHYLO: An integrated easy-to-use pipeline for ML phylogenetic tree inference

abc-fdss

ABC framework based on the distribution of segregationg sites between populations and Random Forest to perform model choice

admixture_cv_sum

[DEPRECATED] Summarizes the output of cross-validation values for multiple runs of admixture

aftrrad

AftrRAD is a bioinformatic pipeline for analyzing GBS data such as those generated with RADseq.

agat

Another Gtf/Gff Analysis Toolkit

al2prunedtree

Prunes a given newick tree file to keep only taxa present in a given sequence alignment (FASTA format)

alvis

amas

Calculate summary statistics and manipulate multiple sequence alignments

amp_alignment_process

A workflow and toolkit of perl scripts to manipulate multiple sequence alignments

amplimap

amplicon/smMIP mapping and analysis pipeline

anadiversity

Two modules to identify the SNPs and RNA Editing Sites of Chloroplast Genomes.

ancient_mtdna_pipeline

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

aniclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

annocript

Annocript is a pipeline for the annotation of de-novo generated transcriptomes. It executes BLAST analysis with UniProt, NCBI Conserved Domain Database and Nucleotide divisions, Gene Ontology, UniPathways and the Enzyme Commission. It gives information about the longest ORF (using DNA2PEP) and non-coding potential of the sequences (using Portrait). A final heuristic makes Annocript able to identify putative long non-coding RNAs among your transcripts.

annogesic

ANNOgesic is a bacterial transcriptome annotation pipeline based on RNA-Seq.

arbow

Cultivate your multiple sequence alignments to get better trees

arpir

Automatic RNA-Seq Pipelines with Interactive Report

asgart

A genome-scale, fast, and precise segmental duplications mapping tool

assembly_improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

assemblystats

Run Assembly statistics on a genome assembly (BUSCO and assemblyStats and new_Assemblathon.pl)

astral_pipeline

A pipeline for processing a pyRAD .loci file by performing naive binning, running RAxML, and directing the output into ASTRAL

atacseq

ATAC-seq peak-calling, QC and differential analysis pipeline

avtad

Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).

bamdst

a lightweight bam file depth statistical tool

bgreat2

Paired reads mapping on de Bruijn graph

bhlh_annotator

automatic annotation of bHLH gene family in plants

bind_annotation

Scripts, notes and documents about the BIND annotation workflow (BIND: ab initio gene predictions by BRAKER combined with gene predictions INferred Directly from alignment of RNA-Seq evidence to the genome.)

bio-pipeline

My collection of light bioinformatics analysis pipelines for specific tasks

bioinfo

Various bioinformatics tools

bioinformatics