Jit
Enthusiast computational biologist with business dream !!!
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Kalign: fast multiple sequence alignment program for biological sequences.
By BioStar 2533 days agogithub.com - Kalign is a fast multiple sequence alignment program for biological sequences. Align sequences and output the alignment in MSF format: kalign -i BB11001.tfa -f msf -o out.msf Align sequences and output the alignment in clustal format: kalign...AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome...
By Jit 2440 days agogithub.com - AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for...flexidot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses
By Jit 2358 days agogithub.com - FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...A web-based tool for sequence alignment statistics and innovative visualization
By BioStar 917 days agobioinformatics.um6p.ma - AlignStatPlot, a new R package and online tool that is well-documented and easy-to usefor MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analy-ses on sequencing data and generates new visualisation methods for MSA...LSC: Improving PacBio Long Read Accuracy by Short Read Alignment
By Abhimanyu Singh 2953 days agowww.healthcare.uiowa.edu - Added Command line argument support. Multi-stage execution modes. Support for parallelization. Now execution proceeds in batches of long reads the size of which can be set by --long_read_batch_size N. Better compressed intermediate files. Added...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 2445 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtmiREM: an expectation-maximization approach for prioritizing miRNAs associated with gene-set
By Abhimanyu Singh 2975 days agobioinfo-csi.nus.edu.sg - From list of genes... ... to microRNAs Using established miRNA-interaction databases, miREM combines hypergeometric and expectation-maximization algorithms to sieve through your genetic data for microRNA...HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies
By Jit 3068 days agogithub.com - HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to "just work" with excellent speed and accuracy. We found that previously described haplotype assembly methods are specialized for specific read...SWALO: Scaffolding with assembly likelihood optimization
By Jit 3032 days agoatifrahman.github.io - 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...CONTIGuator !
By BioStar 2561 days agosourceforge.net - CONTIGuator is a Python script for Linux environments whose purpose is to speed-up the bacterial genome assembly process and to obtain a first insight of the genome structure using the well-known artemis comparison tool (ACT).
