Diamonds95

Diamonds95's Stars

• merenlab/anvio

  An analysis and visualization platform for 'omics data

  Language:Python436144

• broadinstitute/GATK-for-Microbes

  Language:wdl226

• linsalrob/PhiSpy

  Prediction of prophages from bacterial genomes

  Language:Jupyter Notebook7021

• CJ-Chen/TBtools-II

  GUI/CommandLine Tool Box for biologistists to utilize NGS data.

  Language:Shell894187

• mummer4/mummer

  Mummer alignment tool

  Language:C++454107

• bioconvert/bioconvert

  Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

  Language:Python36644

• labgem/PPanGGOLiN

  Build a partitioned pangenome graph from microbial genomes

  Language:Python23928

• Arkadiy-Garber/FeGenie

  HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes

  Language:Python5411

• biocommons/biocommons.seqrepo

  non-redundant, compressed, journalled, file-based storage for biological sequences

  Language:Python3935

• germs-lab/ref_soil

  Language:Python108

• bacteria-archaea-traits/bacteria-archaea-traits

  A synthesis of bacterial and archaeal phenotypic trait data

  Language:R3011

• kblin/ncbi-genome-download

  Scripts to download genomes from the NCBI FTP servers

  Language:Python943175

• alexcritschristoph/MicrobialGenomicsScripts

  A selection of short scripts for analyzing microbial genomes

  Language:Python156

• andrewgull/MGERT

  Mobile Genetic Elements Retrieving Tool

  Language:Python155

• bhattlab/MGEfinder

  A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

  Language:Python10916

• tseemann/prokka

  :zap: :aquarius: Rapid prokaryotic genome annotation

  Language:Perl830225

• tonig-evo/workshop-popgenome

  Tutorial about R package PopGenome

  3912

• harrisonlab/popgen

  Population genetics analyses

  Language:C2211

• PatrickKueck/FASconCAT-G

  FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences. FASconCAT-G implemented process options can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.

  Language:Perl3320

• kussell-lab/mcorr

  Inferring bacterial recombination rates from large-scale sequencing datasets.

  Language:Go418

• KlausVigo/phangorn

  Phylogenetic analysis in R

  Language:R20338

• kwongj/maskrc-svg

  Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

  Language:Python186

• veg/hyphy

  HyPhy: Hypothesis testing using Phylogenies

  Language:HyPhy21169

• rderelle/Broccoli

  orthology assignment using phylogenetic and network analyses

  Language:Python42

• Wyss/mauve-py

  Python wrappers for a fork of progressiveMauve multiple genome aligner

  Language:C++72

• stamatak/standard-RAxML

  Language:C328193

• inab/trimal

  A tool for automated alignment trimming in large-scale phylogenetic analyses. Development version: 2.0

  Language:C++17241

• davidemms/OrthoFinder

  Phylogenetic orthology inference for comparative genomics

  Language:Python691187

• hahnlab/CAFE

  Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.

  Language:C++11236

• nylander/catfasta2phyml

  Concatenates FASTA formatted files to one "phyml" (PHYLIP) formatted file

  Language:Perl6422