Alternatives and similar repositories for phyphy

Users that are interested in phyphy are comparing it to the libraries listed below

• uio-cels / NucDiff
  In-depth characterization and annotation of differences between two sets of DNA sequences
  ☆63Updated 5 years ago
• blaxterlab / blobology
  Tools for making blobplots or Taxon-Annotated-GC-Coverage plots (TAGC plots) to visualise the contents of genome assembly data sets as a …
  ☆47Updated 3 years ago
• rderelle / Broccoli
  orthology assignment using phylogenetic and network analyses
  ☆49Updated last month
• genomeannotation / GAG
  Generates an NCBI .tbl file of annotations on a genome.
  ☆68Updated 7 years ago
• clwgg / nQuire
  A statistical framework for ploidy estimation using NGS short-read data
  ☆62Updated 7 years ago
• balabanmetin / uDance
  ☆42Updated last year
• simonwhelan / prequal
  PREQUAL: a pre-alignment quality filter for comparative sequence analyses
  ☆32Updated 3 years ago
• PacificBiosciences / bam2fastx
  Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.
  ☆39Updated 2 years ago
• xfengnefx / hifiasm-meta
  hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads.
  ☆68Updated 2 weeks ago
• harta55 / EnTAP
  EnTAP is moving to GitLab for future changes https://gitlab.com/PlantGenomicsLab/EnTAP
  ☆41Updated 10 months ago
• evolbioinfo / booster
  ☆28Updated 5 years ago
• lbcb-sci / ra
  Assembler for raw de novo genome assembly of long uncorrected reads.
  ☆36Updated 5 years ago
• ibest / ARC
  Assembly by Reduced Complexity (ARC)
  ☆42Updated 9 years ago
• jessiewu / bacterialGWAS
  A pipeline for performing genome-wide association tests for bacterial genomes.
  ☆27Updated 7 years ago
• infspiredBAT / Circoletto
  visualising sequence similarity with Circos
  ☆41Updated 6 years ago
• josephhughes / Sequence-manipulation
  A range of different perl scripts for manipulating sequences, conducting alignments, consensus sequences, changing formats
  ☆30Updated 2 years ago
• AliTVTeam / AliTV
  Visualize whole genome alignments as linear maps
  ☆74Updated 4 months ago
• HuffordLab / GenomeQC
  ☆33Updated 4 years ago
• rki-mf1 / clean
  A nextflow pipeline for decontamination of short reads, long reads and contigs
  ☆55Updated 5 months ago
• gengit / PosiGene
  ☆26Updated 4 years ago
• LANL-Bioinformatics / PhaME
  Given a reference, PhaME extracts SNPs from complete genomes, draft genomes and/or reads. Uses SNP multiple sequence alignment to constr…
  ☆33Updated 2 years ago
• rnajena / poseidon
  PoSeiDon: positive selection detection and recombination analysis pipeline
  ☆38Updated 2 months ago
• cboursnell / crb-blast
  Conditional Reciprocal Best Blast
  ☆42Updated 8 years ago
• ridgelab / JustOrthologs
  ☆35Updated 2 years ago
• veg / hyphy-analyses
  HyPhy standalone analyses
  ☆49Updated 3 months ago
• BenoitMorel / ParGenes
  A massively parallel tool for model selection and tree inference on thousands of genes
  ☆50Updated last year
• thackl / minidot
  Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
  ☆76Updated 9 years ago
• PacificBiosciences / kineticsTools
  Tools for detecting DNA modifications from single molecule, real-time sequencing data
  ☆26Updated 3 years ago
• sanger-pathogens / gff3toembl
  Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI
  ☆29Updated 7 years ago
• KorfLab / CEGMA_v2
  The final version 2 release of our software to detect core genes in eukaryotic genomes
  ☆29Updated 10 years ago