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Software and data repository for PNAS paper 2019.
Amalgamated likelihood estimation (ALE) is a probabilistic approach to exhaustively explore all reconciled gene trees that can be amalgamated as a combination of clades observed in a sample of gene trees. We implement the ALE approach in the context of a reconciliation model (cf. http://arxiv.org/abs/1211.4606 ), which allows for the duplication, transfer and loss of genes. We use ALE to efficiently approximate the sum of the joint likelihood over amalgamations and to find the reconciled gene tree that maximizes the joint likelihood among all such trees.
Calculate summary statistics and manipulate multiple sequence alignments
Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
Assembly statistic visualisation
Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.
Genome annotation with AUGUSTUS
A powerful toolset for genome arithmetic.
R package to calculate unigram and bigram frequencies of English words.
BWK awk modified for biological data
Various bioinformatics tools
convert a blast output to a bed file
Compiled and pretty version of labs
SV detection from paired end reads mapping
Characterizing the evolution of an original network X into an augmented network Y by counting the number of Breakthroughs, Roadblocks, Impasses, Detours, Equal paths and Shortcuts (BRIDES) in the network Y.
Utility script to construct species phylogenies using BUSCO results
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
Official home of genome aligner based upon notion of Cactus graphs
Analyze changes in gene family size and provide a statistical foundation for evolutionary inferences.
Version 5 of the CAFE phylogenetics software
Protein structure comparison tools such as SSAP and SNAP
Automatically exported from code.google.com/p/cdhit
a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
Colibri core is an NLP tool as well as a C++ and Python library for working with basic linguistic constructions such as n-grams and skipgrams (i.e patterns with one or more gaps, either of fixed or dynamic size) in a quick and memory-efficient way. At the core is the tool ``colibri-patternmodeller`` whi ch allows you to build, view, manipulate and query pattern models.
Composite gene families detection
A cross-platform Graphical Analysis Tool for high-throughput CRISPR-based genome editing evaluation
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.