Python library to facilitate genome assembly, annotation, and comparative genomics
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Updated
Sep 6, 2024 - Python
Python library to facilitate genome assembly, annotation, and comparative genomics
A genome visualization python package for comparative genomics
Guided synteny alignment between duplicated genomes (within specified quota constraint)
CoGe (Comparative Genomics) Platform
Command-line program to wrap dagchainer and combine pairwise results into multi-alignments in column format
Federating genomes with love (and synteny derived from functional annotations)
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Synteny Mapping and Analysis Program
Lightweight single-html-file-based Genome Segments playground for Visualize genome features cluster(gene arrow map or other features), add synteny among genome fragments or add crosslink among features, add short(PE/MP)/long reads(pacbio or nanopore) mapping or snpindel in vcf(not support complex sv yet), support all CIGAR of sam alignment, dire…
An R package to infer and analyze synteny networks from protein sequences
CLfinder-OrthNet, a pipeline to encode orthologs from multiple genomes and their evolutionary history into networks (OrthNets) based on co-linearity between them. OrthNets enable detection of all orthologous gene groups that share the same evolutionary history, using a search based on network topology
Trace intervals between genomes using a synteny map
A Java Desktop application with a graphical user interface for the discovery of colinear syntenic blocks across thousands microbial genomes
Pipelines for the production of Treeval data
A visualization tool for viewing MCscanX Synteny Collinearity files (outdated please check description or readme)
Pairwise genome comparison pipeline using the LAST software to align a list of query genomes to a target genome, and plot the results
Pipeline to prepare alignments for visualization with ACT (goo.gl/1T28jX) and for locating possible inter-chromosomal re-arrengments/misjoints
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