This is the Linux app named GeneMiner whose latest release can be downloaded as GeneMiner_win64_20250709.zip. It can be run online in the free hosting provider OnWorks for workstations.
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GeneMiner
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DESCRIPTION
GeneMiner2 is based on our previously developed GeneMiner and Easy353 software and integrates excellent tools such as Blast, Minimap2, Fasttree, Muscle5, Mafft, Astral, PPD, PGA, NOVOPlasty, and OrthoFinder. Please cite the literature prompted by the software when using the corresponding functionalities.
Our GeneMiner2 manuscript is currently under review:
Yu XY, Tang ZZ, Zhang Z, Song YX, He H, Shi Y, Hou JQ, Yu Y. GeneMiner2: Accurate and automated recovery of genes from genome-skimming data. Manuscript submitted, 2025.
Until that paper is formally published, please cite our earlier work instead:
Zhang Z, Xie PL, Guo YL, Zhou WB, Liu EY, Yu Y. 2022. Easy353: A tool to get Angiosperms353 genes for phylogenomic research. Molecular Biology and Evolution 39(12): msac261.
Xie PL, Guo YL, Teng Y, Zhou WB, Yu Y. 2024. GeneMiner: A tool for extracting phylogenetic markers from next-generation sequencing data. Molecular Ecology Resources e139.
Features
- target gene assembly
- phylogenetic reconstruction
This is an application that can also be fetched from https://sourceforge.net/projects/geneminer/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
