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
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