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quicktree
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public |
Fast implementation of the neighbour-joining phylogenetic inference method
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2024-12-14 |
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ucsc-qactoqa
|
public |
convert from compressed to uncompressed
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2024-12-14 |
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ropebwt2
|
public |
Incremental construction of FM-index for DNA sequences
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2024-12-14 |
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newick_utils
|
public |
The Newick Utilities are a suite of Unix shell tools for processing phylogenetic trees. We distribute the package under the BSD License. Functions include re-rooting, extracting subtrees, trimming, pruning, condensing, drawing (ASCII graphics or SVG).
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2024-12-14 |
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r-intego
|
public |
An unsupervised gene clustering algorithm based on the integration of external biological knowledge, such as Gene Ontology annotations, into expression data.
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2024-12-14 |
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htslib
|
public |
C library for high-throughput sequencing data formats.
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2024-12-14 |
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ucsc-genepredtoprot
|
public |
create protein sequences by translating gene annotations
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2024-12-14 |
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wgsim
|
public |
No Summary
|
2024-12-14 |
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atac
|
public |
No Summary
|
2024-12-14 |
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ucsc-bedpileups
|
public |
Find (exact) overlaps if any in bed input
|
2024-12-14 |
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py2bit
|
public |
A package for accessing 2bit files using lib2bit
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2024-12-14 |
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cansam
|
public |
C++ binding for SAM/BAM files
|
2024-12-14 |
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perl-time-hires
|
public |
High resolution alarm, sleep, gettimeofday, interval timers
|
2024-12-14 |
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bowtie
|
public |
An ultrafast memory-efficient short read aligner
|
2024-12-14 |
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perl-digest-sha1
|
public |
Perl interface to the SHA-1 algorithm
|
2024-12-14 |
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ucsc-fatrans
|
public |
Translate DNA .fa file to peptide
|
2024-12-14 |
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ucsc-checkagpandfa
|
public |
takes a .agp file and .fa file and ensures that they are in synch
|
2024-12-14 |
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perl-unicode-normalize
|
public |
Unicode Normalization Forms
|
2024-12-14 |
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ucsc-mafmefirst
|
public |
Move component to top if it is one of the named ones.
|
2024-12-14 |
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fasttree
|
public |
FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences
|
2024-12-14 |
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ucsc-chainantirepeat
|
public |
Get rid of chains that are primarily the results of repeats and degenerate DNA
|
2024-12-14 |
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ucsc-hgsqldump
|
public |
Execute mysqldump using passwords from .hg.conf
|
2024-12-14 |
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perl-unicode-map
|
public |
Map charsets from and to UTF-16 unicode
|
2024-12-14 |
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ucsc-mafspecieslist
|
public |
Scan maf and output all species used in it.
|
2024-12-14 |
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ucsc-pslrc
|
public |
reverse-complement psl
|
2024-12-14 |
|
meraculous
|
public |
Meraculous is a whole genome assembler for Next Generation Sequencing data, geared for large genomes. It's hybrid k-mer/read-based approach capitalizes on the high accuracy of Illumina sequence by eschewing an explicit error correction step which we argue to be redundant with the assembly process. Meraculous achieves high performance with large datasets by utilizing lightweight data structures and multi-threaded parallelization, allowing to assemble human-sized genomes on a high-cpu cluster in under a day. The process pipeline implements a highly transparent and portable model of job control and monitoring where different assembly stages can be executed and re-executed separately or in unison on a wide variety of architectures.
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2024-12-14 |
|
hisat2
|
public |
Graph-based alignment of next generation sequencing reads to a population of genomes.
|
2024-12-14 |
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ucsc-bedgraphpack
|
public |
Pack together adjacent records representing same value.
|
2024-12-14 |
|
perl-convert-binary-c
|
public |
Binary Data Conversion using C Types
|
2024-12-14 |
|
parafly
|
public |
Given a file containing a list of unix commands, multithreading is used to process the commands in parallel on a single server. Success/failure is captured, and failed commands are retained and reported.
|
2024-12-14 |
|
phyml
|
public |
Phylogenetic estimation using (Maximum) Likelihood
|
2024-12-14 |
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ucsc-maftoaxt
|
public |
Convert from maf to axt format
|
2024-12-14 |
|
irfinder
|
public |
Intron Retention Finder
|
2024-12-14 |
|
ucsc-genepredtobed
|
public |
Convert from genePred to bed format. Does not yet handle genePredExt
|
2024-12-14 |
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ucsc-chaintopslbasic
|
public |
Basic conversion chain file to psl format
|
2024-12-14 |
|
structure
|
public |
The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
|
2024-12-14 |
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sfs_code
|
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.
|
2024-12-13 |
|
r-chbutils
|
public |
Useful utility functions used at the Harvard Chan School Bioinformatics core
|
2024-12-13 |
|
deploid
|
public |
A software that deconvolutes mixed genomes with unknown proportions.
|
2024-12-13 |
|
ucsc-bigwigcorrelate
|
public |
Correlate bigWig files, optionally only on target regions.
|
2024-12-13 |
|
ucsc-ticktodate
|
public |
Convert seconds since 1970 to time and date
|
2024-12-13 |
|
kaiju
|
public |
Fast and sensitive taxonomic classification for metagenomics
|
2024-12-13 |
|
r-rubic
|
public |
No Summary
|
2024-12-13 |
|
smhasher
|
public |
No Summary
|
2024-12-13 |
|
ucsc-chromgraphtobin
|
public |
Make binary version of chromGraph.
|
2024-12-13 |
|
ucsc-chainprenet
|
public |
Remove chains that don't have a chance of being netted
|
2024-12-13 |
|
zerone
|
public |
Zerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them.
|
2024-12-13 |
|
perl-math-cdf
|
public |
Generate probabilities and quantiles from several statistical probability functions
|
2024-12-13 |
|
ngmlr
|
public |
ngmlr is a long-read mapper designed to align PacBio or Oxford Nanopore reads to a reference genome and optimized for structural variation detection
|
2024-12-13 |
|
takeabreak
|
public |
tool that can detect inversion breakpoints directly from raw NGS reads, without the need of any reference genome and without de novo assembling the genomes
|
2024-12-13 |
