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ALPHA: A Toolkit for Automated Local Phylogenomic Analyses
By Jit 2470 days agogithub.com - Automated Local Phylogenomic Analyses, or ALPHA, is a python-based application that provides an intuitive user interface for phylogenetic analyses and data visualization. It has four distinct modes that are useful for different types of phylogenetic...alien_index : identify potential contaminants or horizontally transferred genes in transcriptomes.
By Jit 1788 days agogithub.com - identify potential contaminants or horizontally transferred genes in transcriptomes. algorithm is based on alogorithm described in the following: Gladyshev, Eugene A., Matthew Meselson, and Irina R. Arkhipova. "Massive horizontal gene transfer in...DEG 5.0: a database of essential genes in both prokaryotes and eukaryotes
By Rahul Nayak 1366 days agowww.essentialgene.org - Essential genes are those indispensable for the survival of an organism, and their functions are therefore considered a foundation of life. Determination of a minimal gene set needed to sustain a life form, a fundamental question in biology, plays a...Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
By LEGE 308 days agogithub.com - Orthoflow is a workflow for phylogenetic inference of genome-scale datasets of protein-coding genes. Our goal was to make it straightforward to work from a combination of input sources including annotated contigs in Genbank format and FASTA files...Fourth Branch of Life
By Jitendra Narayan 4124 days agoNewly Found Pandoraviruses Hint at a Fourth Branch of LifeclusterProfiler
By Jit 3113 days agowww.bioconductor.org - statistical analysis and visulization of functional profiles for genes and gene clustersBioconductor version: Release (3.3)This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.Author:...DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies
By Shruti Paniwala 1818 days agogithub.com - DeCoSTAR computes adjacency evolutionary scenarios using a scoring scheme based on a weighted sum of adjacency gains and breakages. Solutions, both optimal and near-optimal, are sampled according to the Boltzmann–Gibbs distribution centered...Public Databases for Bioinformatics !
By Jit 1373 days agomitra.stanford.edu - https://www.nature.com/articles/s41467-020-17155-yServer Infrastructure: File Server: dhara: Synology 3614 Storage Appliance 4 Core Xeon 108TB disk storage 10Gb ethernet to SCG3 Access atx: dhara:5000 Has btsync server (try it - its much...Ribbon: Visualizing complex genome alignments and structural variation:
By Jit 2583 days agohttp://genomeribbon.com/ - Ribbon can be used for long reads, short reads, paired-end reads, and assembly/genome alignments. Instructions for each data format are available by clicking on "instructions" in each tab on the right. Local installation: You can install Ribbon...String graph based genome assembly software and tools !
By Rahul Nayak 2562 days agoIn graph theory, a string graph is an intersection graph of curves in the plane; each curve is called a "string". String graphs were first proposed by E. W. Myers in a 2005 publication.
