Perlprimer | Design primers for PCR and sequencing Paml | PAML: Phylogenetic Analysis by Maximum Likelihood Pal2nal | Create a codon-based DNA alignment Ncbi-blast | Basic Local Alignment Search Tool Muscle | A multiple sequence alignments program Mrbayes | Bayesian Inference of Phylogeny MkDSSP | A program that calculates DSSP entries from PDB entries Megax | Molecular Evolutionary Genetics Analysis
Meme-suite | Motif based sequence analysis tools Meme-db-tgene | MEME Suite T-gene databases Meme-db-motif | MEME Suite motif databases Mafft | A multiple sequence alignment program Kraken | Assign taxonomic labels to short DNA sequences Jellyfish_k-mer | A tool for counting of k-mers in DNA Jalview | A Sequence Alignment Editor and Viewer Isoelectric-point | Isoelectric point calculator
Amplifx software#
Iqtree | Efficient and versatile phylogenomic software by ML Io_lib | Provides a trace file reading interface Hyphy | Hypothesis Testing using Phylogenies Genpak | Utilities to manipulate DNA sequences
Genometools | collection of bio-informatics tools Geneconv | Statistical Tests for Detecting Gene Conversion WEVOTE | WEighted VOting Taxonomic idEntificationĪline | A Sequence Alignment Editor and ViewerĪmplicon | Design PCR primers on aligned sequencesĪmplifx | Manage, test and design your primers for PCRĪrchaeopteryx | Visualise, analyse and edit phylogenetic treesīedGraphToBigWig | Convert bedGraph to bigWig fileīedtools | A powerful toolset for genome arithmeticīiopython | A set of Python tools for biological computationīowtie | A short read aligner of DNA sequencesīowtie2-legacy | A tool for aligning sequencing readsīpp-phyl-omics | Bio++ Phylogenetic Omics Libraryīpp-popgen | Bio++ Population Genetics Libraryīpp-seq-omics | Bio++ Sequence Omics Libraryīpp1.9-numcalc | Bio++ 1.9 NumCalc LibraryĬistrome-CEAS | CEAS: Cis-regulatory Element Annotation SystemĬistrome-MACS | MACS: Model-based Analysis of ChIP-SeqĬistrome-conductGO | Find the top-n highest expressed TFsĬistrome-extra | Cistrome Applications Harvard extra appsĬistrome-mdseqpos | Cistrome Applications Harvard mdseqposĬlark-ugene | Ugene’s forked CLAssifier based on Reduced K-mersĬlustalx | Multiple Sequence Alignment GUIĬufflinks | A reference-guided assembler for RNA-Seq experimentsĬutadapt | Trim adapters from high-throughput sequencing readsĭatamash | Basic numeric, textual and statistical operationsĭiamond | A sequence aligner for protein and translated DNAĮxonerate | A generic tool for sequence alignment TreeGraph | A feature rich phylogenetic tree editor
SeqMonk | A Mapped Sequence Analysis tool RepeatMasker | Screen DNA sequence for interspersed repeats RAxML | Randomized Axelerated Maximum Likelihood PhyML | Phylogenetic estimation using Maximum Likelihood MetaPhlAn2 | Metagenomic Phylogenetic Analysis HMMER | Biosequence analysis using profile hidden Markov models Gblocks | Select blocks of evolutionarily conserved sites I am grateful for the help I received from the SlackBuilds community! If you have any comments, suggestions or just want to discuss some of the entries, please let me know.ĬAFS_divergence | Clustering Analysis of Functional ShiftsĬAPS_coevolution | Coevolution Analysis using Protein SequencesĭendroPy | A Phylogenetic Computing LibraryĮMBOSS | European Molecular Biology Open Software Suite The latest submission and updates can be viewed here.
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