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Online resources on must-read papers in evolutionary biology, for a literature club
By Shruti Paniwala 878 days agoonline resources on must-read papers in evolutionary biology, for a literature clubAVID: A Global Alignment Program
By Archana Malhotra 2739 days agowww.ncbi.nlm.nih.gov - A new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the...GffCompare: Program for processing GTF/GFF files
By Jit 1963 days agoccb.jhu.edu - The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the “query” files), when compared with a reference annotation (also provided as GFF).Opera: An optimal genome scaffolding program
By Jit 2552 days agosourceforge.net - Opera (Optimal Paired-End Read Assembler) is a sequence assembly program (http://en.wikipedia.org/wiki/Sequence_assembly ). It uses information from paired-end or long reads to optimally order and orient contigs assembled from...MCMCTREE: a phylogenetic program for Bayesian estimation of species divergence times
By Poonam Mahapatra 2365 days agowww.fish-evol.com - MCMCTREE is a phylogenetic program for Bayesian estimation of species divergence times using soft fossil constraints under various molecular clock models. This is part of the PAML package. In this tutorial I will analyze an easy...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2146 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...Cactus: a reference-free whole-genome multiple alignment program
By Jit 1929 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...CrossMap: program for genome coordinates conversion between different assemblies
By Rahul Nayak 1032 days ago Comments (1)crossmap.sourceforge.net - CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats...HS3D: Homo Sapiens Splice Sites Dataset
By Jit 1624 days agowww.sci.unisannio.it - HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of...
