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Align-m


bcftools


beast1.10 cpu


beast1.10 gpu


beast1.10 cpu+gpu


BEAST2


bowtie2


bowtie2-build


bwa


bwa-aln


bwa-build


ClustalW2


codeml


ExaML


ExaML-parser


ExaML-raxml


FragGeneScan


GeneMarkS


Glimmer3


Glimmer3-build


hmmbuild


hmmsearch


Kalign2


MAFFT


MetaGeneMark


ModelGenerator


MUSCLE


NxTrim


PartitionFinder

Phylip


PhyML


ProbCons


RAxML


Ray


ReadSeq


samtools-view


SciPhy

Certify that your sequences are amino acid


SciPhy: A Scientific Workflow for Phylogenetic Analyses

SciPhy was designed to construct maximum likelihood phylogenetic trees for amino acid sequences. The SciPhy conceptual workflow is composed by the following main activities: (1) Alignment Construction: with MAFFT, (2) Alignment Format Conversion: with ReadSeq, (3) Best Evolutionary Model Election: with ModelGenerator, and (4) Phylogenetic Tree Construction: with RAxML

SwiftGecko



SwiftGecko: A Scientific Workflow for Genome Comparisons

SwiftGecko identifies collections of high-scoring segment pairs (HSPs) in genomes. The SwiftGecko conceptual workflow is composed by three computational modulesm, covering ten main activities: (I) Dictionary Calculation, for creatimg dictionaries for each sequence, composed by activities: (1) Reverse Complementary Sequence, (2) Words Scanning (3), Words Sorting, and (4) Computing Genome Dictionaries. (II) HSP Detection, for detecting seed points or hits used to identify HSP locations, composed by activities (5) Hits Detection, (6) Hits Sorting, (7) Hits Filtering, (8) Fragment Obtaining, and (9) Combine Fragments. (III) Post-processing Module, for attaching complementary tasks for performing statistical calculations, composed by activity: (10) CSV File Generation.

SPAdes


T-Coffee