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mauve
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public |
Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion
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2023-06-16 |
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barriers
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public |
Compute local minima and energy barriers of a landscape.
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2023-06-16 |
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perl-text-abbrev
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public |
abbrev - create an abbreviation table from a list
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2023-06-16 |
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phyluce
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public |
Software for UCE (and general) phylogenomics.
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2023-06-16 |
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perl-storable
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public |
persistence for Perl data structures
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2023-06-16 |
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sshmm
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public |
ssHMM is an RNA motif finder that recovers sequence-structure motifs from RNA-binding protein data, such as CLIP-Seq data.
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2023-06-16 |
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tardis
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public |
Pre-processor for bioinformatics cluster job submission
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2023-06-16 |
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gbsx
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public |
Toolkit for experimental design and demultiplexing genotyping by sequencing experiments
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2023-06-16 |
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icount
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public |
Computational pipeline for analysis of iCLIP data
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2023-06-16 |
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biopet-basecounter
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public |
BaseCounter counts the bases from genes and transcripts and outputs information on the counts in exonic and intronic regions as well as information on the counts on the sense and antisense strands.
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2023-06-16 |
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mauvealigner
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public |
The mauveAligner and progressiveMauve command-line tools for generating multiple genome alignments in the presence of large-scale evolutionary events
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2023-06-16 |
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phenix
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public |
Public Health England SNP calling pipeline
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2023-06-16 |
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pathwaymatcher
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public |
PathwayMatcher is a software tool writen in Java to search for pathways related to a list of proteins in Reactome.
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2023-06-16 |
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mirge
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public |
comprehensive analysis of miRNA sequencing data
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2023-06-16 |
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libmems
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public |
libMems is a freely available software development library to support DNA string matching and comparative genomics.
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2023-06-16 |
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biopet-seqstat
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public |
SeqStat is a package that contains tools to generate stats from a FastQ file, merge those stats for multiple samples, and validate the generated stats files.
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2023-06-16 |
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metaquant
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public |
Quantitative microbiome analysis
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2023-06-16 |
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perl-string-random
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public |
Perl module to generate random strings based on a pattern
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2023-06-16 |
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r-ngsplot
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public |
Quick mining and visualization of NGS data by integrating genomic databases
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2023-06-16 |
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ngsplotdb-ngsplotdb-hg19
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public |
HG19 genome database for NGSplot
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2023-06-16 |
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atactk
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public |
A toolkit for working with ATAC-seq data.
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2023-06-16 |
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r-ngsplotdb-hg19
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public |
HG19 genome database for NGSplot
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2023-06-16 |
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fastq-anonymous
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public |
Change the sequence of a fastq file to enable sharing of confidential information, for troubleshooting of tools.
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2023-06-16 |
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perl-file-util
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public |
Easy, versatile, portable file handling
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2023-06-16 |
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r-ngsplotdb-mm10
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public |
MM10 genome database for NGSplot
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2023-06-16 |
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biopet-fastqsplitter
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public |
This tool divides a fastq file into smaller fastq files, based on the number of output files specified.
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2023-06-16 |
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deepvariant
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public |
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data
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2023-06-16 |
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irida-sistr-results
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public |
Exports SISTR results available through IRIDA into a single report.
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2023-06-16 |
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r-ngsplotdb-hg38
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public |
HG19 genome database for NGSplot
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2023-06-16 |
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pmdtools
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public |
Compute postmortem damage patterns and decontaminate ancient genomes
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2023-06-16 |
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fasta-splitter
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public |
Divides a large FASTA file into a set of smaller, approximately equally sized files
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2023-06-16 |
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pyvolve
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public |
Pyvolve is an open-source Python module for simulating sequences along a phylogenetic tree according to continuous-time Markov models of sequence evolution. Please cite: Spielman, S.J., and Wilke, C.O. (2015). Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies. PLOS ONE 10, e0139047.
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2023-06-16 |
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genomestrip
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public |
Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data
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2023-06-16 |
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lorikeet
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public |
Tool for digital spoligotyping of MTB strains from Illumina read data
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2023-06-16 |
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biopet-validatefastq
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public |
This tool validates a FASTQ file.
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2023-06-16 |
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r-pma
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public |
Performs Penalized Multivariate Analysis: a penalized matrix decomposition, sparse principal components analysis, and sparse canonical correlation analysis, described in the following papers: (1) Witten, Tibshirani and Hastie (2009) A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis. Biostatistics 10(3):515-534. (2) Witten and Tibshirani (2009) Extensions of sparse canonical correlation analysis, with applications to genomic data. Statistical Applications in Genetics and Molecular Biology 8(1): Article 28.
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2023-06-16 |
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r-geiger
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public |
Methods for fitting macroevolutionary models to phylogenetic trees.
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2023-06-16 |
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bax2bam
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public |
bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format
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2023-06-16 |
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itero
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public |
A pipeline for iterative, guided contig assembly that integrates spades, bwa, and samtools to produce assembled contigs.
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2023-06-16 |
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r-funrar
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public |
Computes functional rarity indices as proposed by Violle et al. (2017)
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2023-06-16 |
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logol
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public |
Logol is a pattern matching grammar language and a set of tools to search a pattern in a sequence (nucleic or proteic)
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2023-06-16 |
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r-ncbit
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public |
making NCBI taxonomic data locally available and searchable as an R object
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2023-06-16 |
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pisces
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public |
Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
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2023-06-16 |
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r-msm
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public |
Functions for fitting continuous-time Markov and hidden Markov multi-state models to longitudinal data. Designed for processes observed at arbitrary times in continuous time (panel data) but some other observation schemes are supported. Both Markov transition rates and the hidden Markov output process can be modelled in terms of covariates, which may be constant or piecewise-constant in time.
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2023-06-16 |
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r-nodiv
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public |
An implementation of the nodiv algorithm, see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
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2023-06-16 |
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biopet-extractadaptersfastqc
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public |
ExtractAdaptersFastqc reads which adapter sequences where found from a FastQC raw report.
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2023-06-16 |
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r-treesim
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public |
Simulation methods for phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa()), or a fixed age (sim.bd.age()), or a fixed age and number of tips (sim.bd.taxa.age()). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa()). The function sim.bd.age() (and sim.rateshift.taxa() without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot(), LTT.plot.gen() and LTT.average.root(). TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa()). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa() man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim()). (ii) sim.rateshifts.taxa() is generalized to sim.bdsky.stt() for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa(). This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree() simulates coalescent gene trees within birth-death species trees, and sim.genetree() simulates coalescent gene trees.
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2023-06-16 |
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r-aptreeshape
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public |
Simulation and analysis of phylogenetic tree topologies using statistical indices. It is a companion library of the 'ape' package. It provides additional functions for reading, plotting, manipulating phylogenetic trees. It also offers convenient web-access to public databases, and enables testing null models of macroevolution using corrected test statistics. Trees of class "phylo" (from 'ape' package) can be converted easily. Implements methods described in Bortolussi et al. (2005) and Maliet et al. (2017).
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2023-06-16 |
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snpiphy
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public |
An automated snp phylogeny pipeline
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2023-06-16 |
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iclipro
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public |
iCLIPro is a Python package that can be used to control for systematic misassignments in iCLIP data.
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2023-06-16 |
