2676 days ago
String graph based genome assembly software and tools !
...s, which are de Bruijn graph based, SAGE uses the string-overlap graph. SAGE builds upon great existing work on string-overlap graph and maximum likelihood assembly, bringing an importa...2475 days ago
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Bio++ : C Language libraries for your biological need
...files in Phylip format.Distance methods: (U/W)PGMA, NJ, BioNJ.Maximum likelihood (NNI, including a PhyML-like...ariant classes.Covarion models.Model including gaps.Global clock tree likelihood models.Virtually any kind of...4094 days ago
Genome Assembly Tools and Software - PART2 !!
...prior run of PRICE or any other ALE 20130717 – Assembly Likelihood EstimatorALE is a probabalistic framework for determining the likelihood of an assembly given the data...2832 days ago
List of Bioinformatics Software Tools for Next Generation Sequencing
...glfSingle Description: uses likelihood-based model for variant calling, starts from genotype likelihoods that have been computed from...ng data”; Bayesian genotype likelihood model Input: BED or VCF file...genes; Also, “Estimates the likelihood of a particular nonsynonymous...3055 days ago
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ForBio and UiB course: Introduction to phylogenetic methods
...hasis on use of DNA data. Students will learn how to prepare their data, explore its properties and how to analyze it using distance, parsimony, likelihood and Bayesian methods. In the...1748 days ago
Create genome scaffolding with Perl
...} my $preTrim = min($sStart, $lStart); my $postTrim = min($sLen - $sEnd, $lLen - $lEnd); ## Only continue on if there's a good likelihood that this will work ## i...2455 days ago
Perl script to find coding regions in DNA sequences
...three symbols (option g) my @codons = ($seq =~ m/.../g); # the likelihood ratio is for a current triple...at is, 1/64. After this, # the log must be applied to obtain the log-likelihood ratio. # It is recommended t...2301 days ago
Comment on "Bio++ : C Language libraries for your biological need"
...ng to several model of evolution and reconstruction methods).bppML (Optimize a phylogenetic tree and other model parameters according to maximum likelihood. Several models are supported...3972 days ago