Alternatives and similar repositories for pagan2-msa

Users that are interested in pagan2-msa are comparing it to the libraries listed below

• salzberg-lab / bolotie
  SARS-CoV-2: detecting recombinations in viruses using large data sets with high sequence similarity
  ☆13Updated 2 years ago
• deweylab / detonate
  DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation
  ☆14Updated 9 years ago
• EvolBioInf / fur
  Find Unique genomic Regions
  ☆32Updated 2 months ago
• DessimozLab / omamer
  OMAmer - tree-driven and alignment-free protein assignment to sub-families
  ☆22Updated last month
• aesheppard / TETyper
  transposable element typing pipeline
  ☆19Updated last year
• at-cg / mm2-plus
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
  ☆36Updated last month
• nluhmann / BlastFrost
  ☆44Updated 4 years ago
• SR-Martin / alvis
  ☆20Updated 2 years ago
• atifrahman / SWALO
  Scaffolding with assembly likelihood optimization
  ☆21Updated 5 years ago
• MrTomRod / orthofinder-tools
  Tools to process OrthoFinder output: Calculate the most common gene name of an orthogroup by majority vote and create plots analogous to …
  ☆19Updated last year
• bayesiancook / phylobayes
  PhyloBayes: phylogenetic reconstruction using infinite mixtures (CAT and CAT-GTR) -- serial version (for MPI, see pbmpi.git)
  ☆15Updated 4 years ago
• balabanmetin / uDance
  ☆43Updated last year
• TravisWheelerLab / BATH
  Better Alignments with Translated HMMER
  ☆24Updated last week
• svm-zhang / AGOUTI
  Annotated Genome Optimization Using Transcriptome Information
  ☆20Updated 5 years ago
• gengit / PosiGene
  ☆26Updated 4 years ago
• rnajena / poseidon
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆39Updated 3 months ago
• duchene / phylomad
  ☆19Updated last year
• arzwa / Whale.jl
  Bayesian gene tree reconciliation and WGD inference using amalgamated likelihood estimation
  ☆16Updated 8 months ago
• EGTortuero / viga
  De novo VIral Genome Annotator
  ☆23Updated last year
• iqbal-lab-org / varifier
  Variant call verification
  ☆16Updated 7 months ago
• lh3 / treebest
  TreeBeST: Tree Building guided by Species Tree
  ☆14Updated 14 years ago
• karubiotools / getSequenceInfo
  Perl and Python scripts allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories
  ☆14Updated 9 months ago
• alvinxhan / PhyCLIP
  Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
  ☆19Updated 5 years ago
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆33Updated 3 years ago
• simonerampelli / viromescan
  ViromeScan allows the user to explore and taxonomically characterize the virome from metagenomic reads, efficiently denoising samples fro…
  ☆13Updated 2 years ago
• hillerlab / CESAR2.0
  ☆29Updated 3 years ago
• LoadStar822 / Chimera
  Chimera: A Versatile Metagenomic Classification Tool
  ☆20Updated 2 weeks ago
• althonos / pyfastani
  Cython bindings and Python interface to FastANI, a method for fast whole-genome similarity estimation.
  ☆23Updated 2 months ago
• MartinPippel / DAmar
  Long read QC, assembly and scaffolding pipeline
  ☆13Updated 5 years ago
• BrendelGroup / AEGeAn
  Integrated toolkit for analysis and evaluation of annotated genomes
  ☆25Updated 5 months ago