2543 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...2342 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...3961 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...2699 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...2922 days ago
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3932 days ago
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...1615 days ago
Create genome scaffolding with Perl
...} my $preTrim = min($sStart, $lStart); my $postTrim = min($sLen - $sEnd, $lLen - $lEnd); ## Only continue on if there's a good likelihood that this will work ## i...2322 days ago
Perl script to find coding regions in DNA sequences
...three symbols (option g) my @codons = ($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...2168 days ago
SWALO: Scaffolding with assembly likelihood optimization
SWALO (scaffolding with assembly likelihood optimization) is a method for scaffolding based on likelihood of genome assemblies computed using generative models for sequencing. Please email your questions, comments, suggestions, and bug reports to atif.bd@gmail.com.Tags: SWALO, Scaffolding, assembly, likelihood, optimization
2159 days ago
ALE: Assembly Likelihood Estimator
Just import the assembly, bam and ALE scores. You can convert the .ale file to a set of .wig files with ale2wiggle.py and IGV can read those directly. Depending on your genome size you may want to convert the .wig files to the BigWig format.Tags: ALE, Genome, Assembly, Likelihood, Estimator
437 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...3839 days ago