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admixtools
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public |
ADMIXTOOLS (Patterson et al. 2012) is a software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
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2025-04-22 |
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plass
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public |
Plass (Protein-Level ASSembler) and PenguiN (Protein-guided Nucleotide assembler) are methods to assemble short read sequencing data on a protein level to proteins or DNA contigs
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2025-04-22 |
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slimm
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public |
SLIMM - Species Level Identification of Microbes from Metagenomes
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2025-04-22 |
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mtbseq
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public |
Pipeline for WGS analysis of M. tuberculosis
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2025-04-22 |
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perl-bundle-bioperl
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public |
A bundle to install external CPAN modules used by BioPerl 1.5.2
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2025-04-22 |
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bpp-popgen
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public |
Bio++ is a set of C++ libraries for Bioinformatics.
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2025-04-22 |
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red
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public |
Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
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2025-04-22 |
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truvari
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public |
Structural variant comparison tool for VCFs.
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2025-04-22 |
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gatktool
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public |
Functions and classes used to extend a GATK tool with Python
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2025-04-22 |
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metaxa
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public |
Improved Identification and Taxonomic Classification of Small and Large Subunit rRNA in Metagenomic Data.
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2025-04-22 |
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r-metstat
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public |
A diverse collection of metabolomics related statistical tools.
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2025-04-22 |
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r-popgenome
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public |
Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.
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2025-04-22 |
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r-blockfest
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public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
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2025-04-22 |
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fastani
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public |
FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
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2025-04-22 |
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evidencemodeler
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public |
Evidence Modeler combines ab intio gene predictions, protein alignments, and transcript alignments into weighted consensus gene structures
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2025-04-22 |
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biolib
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public |
Package for common tasks in bioinformatics.
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2025-04-22 |
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kraken2
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public |
Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.
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2025-04-22 |
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smeg
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public |
Strain-level Metagenomic Estimation of Growth rate (SMEG) measures growth rates of microbial strains from complex metagenomic dataset
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2025-04-22 |
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cgatcore
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public |
CGAT : the Computational Genomics Analysis Toolkit
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2025-04-22 |
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dadi
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public |
Fit population genetic models using diffusion approximations to the allele frequency spectrum
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2025-04-22 |
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gdc
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public |
Utility designed for compression of genome collections from the same species.
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2025-04-22 |
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msalign2
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public |
Aligns 2 CE-MS or LC-MS datasets using accurate mass information.
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2025-04-22 |
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r-whopgenome
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public |
Provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
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2025-04-22 |
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poppunk
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public |
PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
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2025-04-22 |
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apt-probeset-summarize
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public |
From Affymetrix Power Tools package. apt-probeset-summarize is program for analyzing expression arrays including 3' IVT and exon arrays. Supports background correction (MAS5,RMA), normalization (linear scaling, quantile, sketch), and summarization (PLIER, RMA, MAS5) methods.
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2025-04-22 |
