Ecosyste.ms: Repos

An open API service providing repository metadata for many open source software ecosystems.

Package Usage: conda: mafft

View more package details: https://packages.ecosyste.ms/registries/anaconda.org/packages/mafft

Dependent Repos 53

ifremer-bioinformatics/samba
Standardized and Automated MetaBarcoding Analyses workflow (Mirror)
  • 7.310 containers/qiime2-2019.10/environment.yml

Size: 109 MB - Last synced: 11 months ago - Pushed: 11 months ago

aglucaci/AnalysisOfOrthologousCollections
  • 7.475.* environment.yml

Size: 289 MB - Last synced: 3 months ago - Pushed: 3 months ago

yatisht/usher
Ultrafast Sample Placement on Existing Trees
  • install/environment.yml

Size: 39.1 MB - Last synced: 13 days ago - Pushed: 13 days ago

bpucker/MYB_annotator
This tool performs an automatic identification, annotation, and analysis of the MYB gene family in plants. It can be applied to new transcriptome of genome assemblies.
  • environment.yml

Size: 2.7 MB - Last synced: over 1 year ago

klamkiew/vegeta
work in progress
  • 7.470.* environment.yml

Size: 223 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

lfnothias/qiime2
  • 7.475.* environment.yml

Size: 21.5 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

timplab/ncov
ncov work
  • environment.yml

Size: 4.17 MB - Last synced: about 2 months ago - Pushed: over 3 years ago

nibscbioinformatics/nanoprofiler
Profiling Nanobodies sequencing libraries
  • 7.471 software/nibscbioinformatics/mafft/environment.yml

Size: 2.43 MB - Last synced: about 1 year ago - Pushed: over 3 years ago

mbbu/arbopan
A pangenomics pipeline tailored for arboviruses.
  • 7.505 environment.yml

Size: 4.21 MB - Last synced: 12 days ago - Pushed: almost 2 years ago

MPI-SHH-SummerSchool/dag-material
  • 7.487.* Hands on Introduction to Ancient Microbiome Analysis/environment.yml

Size: 489 MB - Last synced: 9 months ago - Pushed: over 2 years ago

BCCDC-PHL/mpxv-artic-nf
  • 7.471.* environments/environment.yml

Size: 49.2 MB - Last synced: 24 days ago - Pushed: 11 months ago

evoosa/16S_bacteria_detector
Gets the frequency of bacterias for 16S RRNA sequences using the available algorithms
  • 7.471 src/environment.yml

Size: 97.4 MB - Last synced: about 1 year ago - Pushed: about 3 years ago

HimesGroup/AKR
AKR Superfamily Website
  • data/sequence_processing/environment.yml

Size: 48 MB - Last synced: 5 days ago - Pushed: 5 days ago

vappiah/bacterial-genomics-tutorial
  • environment.yaml

Size: 6.93 MB - Last synced: 10 months ago - Pushed: 10 months ago

clatworthylab/bulkBCRseq
Bulk BCR seq processing pipeline. Reimplementation of original package provided by Dr. Rachael Bashford-Rogers (Oxford)
  • environment.yml

Size: 264 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

amkram/shusher
Private, browser-based placement of genome sequences on phylogenetic trees using UShER.
  • usher-port/environment.yml

Size: 101 MB - Last synced: 12 months ago - Pushed: 12 months ago

bokulich-lab/advanced-comp-bio-tutorial
Hands-on demonstration of 16S rRNA gene sequence analysis for SysBio Advanced Block Course 2022
  • 7.490 environment.yml

Size: 77.9 MB - Last synced: 12 months ago - Pushed: 12 months ago

jbloom/PRJNA692319_public
Analysis of Antarctica sequencing samples contaminated with SARS-CoV-2
  • 7.490.* environment.yml

Size: 13.7 KB - Last synced: about 1 year ago - Pushed: about 2 years ago

omicsclass/biodocker
docker images for bioinformatics
  • 7.471.* ampliseq-q2/environment.yml
  • 7.310.* pop-evol-gwas/environment.yml

Size: 59.2 MB - Last synced: 11 months ago - Pushed: over 1 year ago

ctlab/GScour
Genome-wide detection of positive selection
  • 7.475 environment.yml

Size: 1.89 MB - Last synced: 28 days ago - Pushed: 11 months ago

conda-envs/default
  • environment.yml

Last synced: 12 months ago

polio-nanopore/piranha
  • environment.yml

Size: 34.9 MB - Last synced: about 3 hours ago - Pushed: 12 days ago

BCCDC-PHL/consensus-align-utr-trim
Align SARS-CoV-2 sequences against a reference genome, and trim UTR sequences
  • 7.471.* environments/environment.yml

Size: 19.5 KB - Last synced: 24 days ago - Pushed: almost 3 years ago

juanledesma78/initio_data_processing
INITIO project to study the prevalence of drug resistance affecting the integrase inhibitors among people recently diagnosed with HIV infection in the UK
  • 7.310 environment.yml

Size: 392 KB - Last synced: about 1 year ago - Pushed: over 1 year ago

KathrynCampbell/MADDOG
Method for Assignment, Definition and Designation of Global lineages
  • environment.yml

Size: 23.7 MB - Last synced: 10 months ago - Pushed: 10 months ago

bacpop/BacQuerya-processing
Scripts to process publicly available information for indexing.
  • environment.yml

Size: 36.4 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago

crimBubble/ECCsplorer
The ECCsplorer is a bioinformatics pipeline for the automated detection of extrachromosomal circular DNA (eccDNA) from paired-end read data of amplified circular DNA.
  • environment.yml

Size: 15.9 MB - Last synced: 7 months ago - Pushed: 7 months ago

jbloomlab/pdb_prot_align
Align proteins to chains in PDB structures
  • 7.407.* environment.yml

Size: 8.48 MB - Last synced: 25 days ago - Pushed: almost 4 years ago

NatPombubpa/Qiime2_2022.8_binder
Qiime2_2022.8_binder test
  • 7.505.* environment.yml

Size: 10.7 KB - Last synced: 9 months ago - Pushed: over 1 year ago

ncbi/datasets
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
  • training/cshl-2021/binder/environment.yml

Size: 20.6 MB - Last synced: about 9 hours ago - Pushed: about 10 hours ago

jbloomlab/SARSr-CoV_homolog_survey
Survey of ACE2 binding specificities among SARS-related CoV homologs
  • 7.471 environment.yml

Size: 139 MB - Last synced: 10 months ago - Pushed: about 1 year ago

babelomics/impuSARS
Software tool for the imputation of whole-genome SARS-CoV-2 sequences.
  • 7.490.* conda/environment.yml

Size: 85.2 MB - Last synced: 9 months ago - Pushed: over 1 year ago

jts/ncov-tools
Small collection of tools for performing quality control on coronavirus sequencing data and genomes
  • workflow/envs/environment.yml

Size: 292 KB - Last synced: 18 days ago - Pushed: 18 days ago

jbloomlab/SARS-CoV-2-RBD_Delta
  • environment.yml

Size: 329 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

folkehelseinstituttet/FHI_SC2_Pipeline_Illumina
Bioinformatic pipeline for SARS-CoV-2 sequence analysis
  • 7.407 CommonFiles/artic-ncov2019/environment.yml

Size: 13.3 MB - Last synced: 19 days ago - Pushed: about 2 months ago

AngieHinrichs/usher Fork of yatisht/usher
Ultrafast Sample Placement on Existing Trees
  • environment.yml

Size: 19.4 MB - Last synced: 6 months ago - Pushed: 6 months ago

uc-cdis/gen3-augur
Python CLI for data utils
  • environment.yml

Size: 15.3 MB - Last synced: about 1 year ago - Pushed: over 1 year ago

dms-vep/dms-vep-pipeline
Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
  • 7.508.* environment.yml

Size: 244 MB - Last synced: 26 days ago - Pushed: 8 months ago

fieldima/adequacy_of_PCMs Fork of phylo-lab-usc/fiels_workbench
This repository contains all the scripts for analyzing the adequacy of the most commonly used phylogenetic comparative models for gene expression datasets.
  • 7.505 Normalization_Reanalysis/environment.yml

Size: 350 MB - Last synced: 11 months ago - Pushed: over 1 year ago

lucanest/Phyloformer
Fast and accurate Phylogeny estimation with self-attention Networks
  • 6.861 environment.yml

Size: 7.45 MB - Last synced: 8 months ago - Pushed: 10 months ago

bgruening/usher Fork of yatisht/usher
Ultrafast Sample Placement on Existing Trees
  • environment.yml

Size: 19.5 MB - Last synced: 30 days ago - Pushed: 5 months ago

yceh/usher Fork of yatisht/usher
Ultrafast Sample Placement on Existing Trees
  • install/environment.yml

Size: 20.4 MB - Last synced: 9 days ago - Pushed: 9 days ago

edikedik/lXtractor
Feature extraction library for sequences and structures
  • >=7.508 environment.yml

Size: 4.24 MB - Last synced: 23 days ago - Pushed: about 2 months ago

AGOberprieler/LoCoLotive
A pipeline to extract putative low-copy nuclear loci based on published target capture probe sets and custom reference genomes.
  • 7.475.* environment.yml

Size: 830 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

pedropatraquim/GENOR
GENOR - smORF homologues
  • 7.475.* environment.yml

Size: 79.6 MB - Last synced: 6 months ago - Pushed: about 1 year ago

hivlab/sarscov2-epidemiology 📦
Visualisation of SARS-CoV-2 genomic epidemiology
  • environment.yml

Size: 119 MB - Last synced: about 1 year ago - Pushed: about 1 year ago

ctbautista/MADDOG Fork of KathrynCampbell/MADDOG
Method for Assignment, Definition and Designation of Global lineages
  • environment.yml

Size: 84.7 MB - Last synced: 3 months ago - Pushed: 3 months ago

jbloom/SARS-CoV-2_Shen_et_al
  • 7.487.* environment.yml

Size: 930 KB - Last synced: about 1 year ago - Pushed: over 2 years ago

duncanberger/nxf-BATQual
Bacterial genome assembly, annotation and typing pipeline.
  • 7.515 environment.yaml

Size: 321 KB - Last synced: 10 months ago - Pushed: 10 months ago

liaoherui/StrainAnalyze
StrainAnalyze: a user-friendly bioinformatics pipeline used to analyze given identified bacterial strains in short reads.
  • 7.515 environment.yaml

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

HIVDiversity/clustering_by_hdbscan
create haplotypes of unaligned DNA sequences using kmer counts and hdbscan
  • environment.yaml

Size: 35.2 KB - Last synced: 9 months ago - Pushed: about 4 years ago

lumc-pgx/CCS-Amplicon
Create polished, phased allele sequences from PacBio amplicon data.
  • 7.407.* environment.yaml

Size: 111 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago

MurrellGroup/PORPIDpipeline
A pipeline for long-read UMI/PID sequencing of HIV amplicons.
  • environment.yaml

Size: 86.6 MB - Last synced: 6 months ago - Pushed: over 1 year ago

MullinsLab/chunked_demux
snakemake pipeline to demultiplex PacBio reads using Index sequences added during PCR
  • environment.yaml

Size: 43 KB - Last synced: 9 months ago - Pushed: about 1 year ago

MikeTrizna/binder-qiime
Testing if qiime can be installed and used in Binder
  • 7.310.* environment.yml

Size: 6.84 KB - Last synced: about 2 months ago - Pushed: about 5 years ago

ressy-group/examples/example-partis
Some example setup and usage of partis for antibody annotation and clonal family inference
  • environment.yml

Last synced: about 1 year ago

rambaut/my-example
  • 7.407 environment.yml

Size: 85.9 KB - Last synced: about 1 year ago - Pushed: over 4 years ago

phylo-lab-usc/fiels_workbench
  • 7.490 Mammal_organs/gene_family_phylogenies/environment.yml

Size: 312 MB - Last synced: 11 months ago - Pushed: almost 2 years ago

Hajibabaei-Lab/SCVUC_COI_metabarcode_pipeline
Snakemake bioinformatic pipeline to process COI mtDNA metabarcodes
  • 7.455 environment.yml

Size: 352 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago

waglecn/helD_search
  • environment.yaml

Size: 23.2 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago

aemann01/afribiota
  • 7.475.* environment.yml

Size: 2.04 MB - Last synced: 4 months ago - Pushed: 4 months ago

aemann01/domhain
Impact of HIV on the oral microbiome
  • 7.490.* 2022-HIV_oral_microbiome/environment.yml

Size: 47.5 MB - Last synced: 8 months ago - Pushed: 8 months ago

aemann01/burkina_faso_its
  • 7.475.* environment.yml

Size: 1.63 MB - Last synced: about 1 year ago - Pushed: over 2 years ago

aemann01/rpo_gene
  • 7.471.* environment.yml

Size: 990 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

aemann01/necrobiome
Necrobiome project
  • 7.471.* environment.yml

Size: 25.7 MB - Last synced: 10 months ago - Pushed: 10 months ago

jakobnissen/2021_h3n2
2021 H3N2 project
  • 7.475 environment.yml

Size: 782 KB - Last synced: about 1 year ago - Pushed: about 3 years ago

davelunt/snakemake-phylo
simple snakemake pipeline to create a phylogeny
  • environment.yaml

Size: 140 KB - Last synced: 7 months ago - Pushed: over 4 years ago

PMMAraujo/subtyper_snakemake
  • 7.245.* environment.yaml

Size: 691 KB - Last synced: about 1 year ago - Pushed: about 5 years ago

PMMAraujo/snappy
SNAPPy is a Snakemake pipeline for HIV-1 subtyping by phylogenetic pairing.
  • 7.245.* environment.yaml

Size: 2.77 MB - Last synced: 7 months ago - Pushed: over 4 years ago

mwang87/GNPS_Volatility_Notebooks
  • 7.471.* environment.yml

Size: 14.6 KB - Last synced: about 1 year ago - Pushed: over 3 years ago

AnnaLewan/SimplySAS
AmpliSAS reimplementation
  • 7.487 environment.yml

Size: 2.16 MB - Last synced: 6 months ago - Pushed: over 2 years ago

nlm-irp-jianglab/bioinfo-wwbe
💧 Bioinformatic pipeline for wastewater-based epidemiology project
  • 7.505 environment.yml

Size: 620 KB - Last synced: 7 months ago - Pushed: 12 months ago

aszaryk/convertconda
  • 7.475.* environment.yml

Size: 1000 Bytes - Last synced: 11 months ago - Pushed: about 1 year ago

MolSSI-Education/iqb-crash-course-2023
  • .devcontainer/environment.yml

Size: 1.95 KB - Last synced: about 1 year ago - Pushed: about 1 year ago

hatio/dockerAF
code to build docker containers
  • 01-buildContainer/afscov2-css/environment.yml

Size: 202 KB - Last synced: 11 months ago - Pushed: almost 3 years ago

BCCDC-PHL/cluster-plasmids
A workflow for assessing similarity between a set of plasmid sequences
  • 7.520.* environments/environment.yml

Size: 12.7 KB - Last synced: 24 days ago - Pushed: 11 months ago

AAriam/biotite Fork of biotite-dev/biotite
A comprehensive library for computational molecular biology
  • environment.yml

Size: 151 MB - Last synced: 28 days ago - Pushed: about 1 year ago

Mojusko/biotite Fork of biotite-dev/biotite
A comprehensive library for computational molecular biology
  • environment.yml

Size: 174 MB - Last synced: 10 months ago - Pushed: about 2 years ago

Dayueban/ampliseq Fork of nf-core/ampliseq
16S rRNA amplicon sequencing analysis workflow using QIIME2
  • 7.310.* environment.yml

Size: 229 KB - Last synced: 10 months ago - Pushed: about 5 years ago

Colelyman/kleuren
Find bubbles in the Colored de Bruijn Graph to reconstruct phylogenetic trees
  • 7.245 environment.yml

Size: 8.17 MB - Last synced: about 1 year ago - Pushed: about 5 years ago

trongnhanuit/Phyloformer Fork of lucanest/Phyloformer
Fast and accurate Phylogeny estimation with self-attention Networks
  • 6.861 environment.yml

Size: 13.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

javaweb2019/datahub Fork of vinitra-zz/datahub
JupyterHubs for use by Berkeley enrolled students
  • 7.471.* deployments/biology/image/environment.yml

Size: 66.6 MB - Last synced: 10 months ago - Pushed: about 3 years ago

sudarshangc/biotite Fork of biotite-dev/biotite
A comprehensive library for computational molecular biology
  • environment.yaml

Size: 104 MB - Last synced: 10 months ago - Pushed: over 4 years ago

sethnr/pathag_pipeline Fork of grubaughlab/DENV_pipeline
  • containers/pgcoe_anypipe/environment.yml
  • environment.yml

Size: 592 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

shaneknapp/datahub Fork of berkeley-dsep-infra/datahub
JupyterHubs for use by Berkeley enrolled students
  • 7.471.* deployments/biology/image/environment.yml

Size: 71.4 MB - Last synced: about 9 hours ago - Pushed: about 9 hours ago

ryanlovett/datahub Fork of berkeley-dsep-infra/datahub
JupyterHubs for use by Berkeley enrolled students
  • 7.471.* deployments/biology/image/environment.yml

Size: 71.5 MB - Last synced: 10 days ago - Pushed: 10 days ago

berkeley-dsep-infra/datahub
JupyterHubs for use by Berkeley enrolled students
  • 7.471.* deployments/biology/image/environment.yml

Size: 71.7 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

cov-lineages/hedgehog
Spikey SARS-CoV-2 sequence based lineage set assignment
  • environment.yml

Size: 94.7 MB - Last synced: about 3 hours ago - Pushed: 25 days ago

blab/veme-2022
Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain
  • 7.505.* environment.yml

Size: 2.33 MB - Last synced: 5 months ago - Pushed: 5 months ago

rki-mf1/PanAdapt
  • 7.520.* environment.yml

Size: 14.8 MB - Last synced: about 2 months ago - Pushed: about 2 months ago

unicorn-23/GwasWA
  • 7.520 environment.yml

Size: 75.5 MB - Last synced: 5 months ago - Pushed: 5 months ago

jacksonh1/slim_conservation_orthogroup_generation
  • 7.520 environment.yml

Size: 3.58 MB - Last synced: 27 days ago - Pushed: about 1 month ago

AMC-LAEB/evoFLUtion
Predictability of Frequency Trajectories of Hemagglutinin Amino Acid Substitutions in Seasonal Influenza A/H3N2 Viruses
  • 7.508.* environment.yml

Size: 4.26 MB - Last synced: 3 months ago - Pushed: 3 months ago

danielpodlesny/samestr
SameStr identifies shared strains between pairs of metagenomic samples based on the similarity of SNV profiles.
  • 7.515.* environment.yml

Size: 239 KB - Last synced: 20 days ago - Pushed: 20 days ago

dms-vep/SARS-CoV-2_XBB.1.5_spike_DMS
  • 7.515.* library_design/environment.yml

Size: 537 MB - Last synced: 26 days ago - Pushed: 27 days ago

ZiemertLab/ARTS
Antibiotic Resistant Target Seeker (ARTS)
  • 7.487.* environment.yml

Size: 123 MB - Last synced: 2 months ago - Pushed: 2 months ago

grubaughlab/DENV_pipeline
  • environment.yml

Size: 592 MB - Last synced: about 1 month ago - Pushed: about 1 month ago

rrouz/AncFlow
AncFlow: A snakemake based pipeline for the ancestral sequence reconstruction of clustered phylogenetic subtrees.
  • environment.yml

Size: 4.64 MB - Last synced: 27 days ago - Pushed: about 1 month ago