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sfs_code
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public |
This article introduces a new forward population genetic simulation program that can efficiently generate samples from populations with complex demographic histories under various models of natural selection. The program (SFS_CODE) is highly flexible, allowing the user to simulate realistic genomic regions with several loci evolving according to a variety of mutation models (from simple to context-dependent), and allows for insertions and deletions. Each locus can be annotated as either coding or non-coding, sex-linked or autosomal, selected or neutral, and have an arbitrary linkage structure (from completely linked to independent). © The Author 2008. Published by Oxford University Press. All rights reserved.
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2025-04-22 |
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r-sigqc
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public |
Provides gene signature quality control metrics in publication ready plots. Namely, enables the visualization of properties such as expression, variability, correlation, and comparison of methods of standardisation and scoring metrics.
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2025-04-22 |
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r-fmsb
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public |
Several utility functions for the book entitled "Practices of Medical and Health Data Analysis using R" (Pearson Education Japan, 2007) with Japanese demographic data and some demographic analysis related functions.
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2025-04-22 |
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dawg
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public |
DNA Assembly with Gaps (Dawg) is an application designed to simulate the evolution of recombinant DNA sequences in continuous time based on the robust general time reversible model with gamma and invariant rate heterogeneity and a novel length-dependent model of gap formation.
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2025-04-22 |
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seqyclean
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public |
Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
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2025-04-22 |
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fast5seek
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public |
Get paths for fast5 files contained in BAM, SAM, or fastq.
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2025-04-22 |
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forgi
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public |
RNA Graph Library
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2025-04-22 |
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dig2
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public |
dig2 is a simple but flexible in silico digester of protein sequences in the FASTA format. It allows for almost any enzyme to be simulated, including MS/MS enzymes to generate CID or ECD/ETD fragments.
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2025-04-22 |
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gretel
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public |
An algorithm for recovering haplotypes from metagenomes
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2025-04-22 |
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bibliospec
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public |
The BiblioSpec Spetral Library tool suite
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2025-04-22 |
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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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2025-04-22 |
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rnaclust
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public |
A tool for clustering of RNAs based on their secondary structures using LocARNA
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2025-04-22 |
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biopet-vcfstats
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public |
Vcfstats is a tool that can generate metrics from a vcf file.
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2025-04-22 |
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bioconductor-interest
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public |
Intron-Exon Retention Estimator
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2025-04-22 |
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akt
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public |
Ancestry and Kinship Tools (AKT)
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2025-04-22 |
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staramr
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public |
Scan genome contigs against the ResFinder and PointFinder databases
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2025-04-22 |
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mustang
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public |
Mustang is a program that implements an algorithm for structural alignment of multiple protein structures.
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2025-04-22 |
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perl-perl4-corelibs
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public |
libraries historically supplied with Perl 4
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2025-04-22 |
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ac-diamond
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public |
AC-DIAMOND is a DNA-protein alignment tool
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2025-04-22 |
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hanselx
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public |
A graph-inspired data structure for determining likely chains of sequences from breadcrumbs of evidence
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2025-04-22 |
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desman
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public |
De novo Extraction of Strains from MetAgeNomes
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2025-04-22 |
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perl-socket
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public |
networking constants and support functions
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2025-04-22 |
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r-stampp
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public |
Allows users to calculate pairwise Nei's Genetic Distances (Nei 1972), pairwise Fixation Indexes (Fst) (Weir & Cockerham 1984) and also Genomic Relationship matrixes following Yang et al. (2010) in mixed and single ploidy populations. Bootstrapping across loci is implemented during Fst calculation to generate confidence intervals and p-values around pairwise Fst values. StAMPP utilises SNP genotype data of any ploidy level (with the ability to handle missing data) and is coded to utilise multithreading where available to allow efficient analysis of large datasets. StAMPP is able to handle genotype data from genlight objects allowing integration with other packages such adegenet. Please refer to LW Pembleton, NOI Cogan & JW Forster, 2013, Molecular Ecology Resources, 13(5), 946-952. <doi
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2025-04-22 |
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r-pegas
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public |
Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.
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2025-04-22 |
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r-qorts
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public |
QoRTs toolkit for analysis, quality control, and data management of RNA-Seq
datasets.
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2025-04-22 |
