Python library to facilitate genome assembly, annotation, and comparative genomics
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Updated
Jul 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)
Genome assembly scaffolding using information from paired-end/mate-pair libraries, long reads, and synteny to closely related species.
Query sequence database by HMMs arranged in predefined synteny structure
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
Pipeline to create phage genome synteny graphics from genbank files
Run and compare algorithms for phylogenetic reconciliation and super-reconciliation
AKRUP: ancestral karyotype reconstruction universal pipeline
Custom scripts and workflows used in the genomics and population analysis of oat crown rust (Puccinia coronata f. sp. avenae) preprint (bioRxiv 2023.09.18.557855). All steps performed in Linux environment or R.
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