A phylogenomics resource for the marine diatom Pseudo-nitzschia multistriata
Description
The resource contains phylogenetic trees built from approximately 9000 P. multistriata genes, comparing them to their orthologs (over 2 million sequences) across major taxa of archaea, bacteria and eukaryotes (Basu et al., 2017). For each orthologous group a tree is built twice using two different substitution models. Each sequence within a tree is given a specific ID which is a combination of a unique number along with a taxonomy code, for example "alla_stramenopile|34" signifies 1) alla: organism Albugo laibachii. 2) stramenopile: broad taxonomic class. 3) 34: protein ID for Albugo laibachii DNA topoisomerase 2. The mapping between Pseudo-nitzschia multistriata proteins and the phylogenetic trees is present in the file "p.multistriata_gene_tree.txt". The detailed description of each protein ID given in any phylogenetic tree is present in the file "geneDB.txt". The phylogenetic trees generated using JTT and WAG substitution models of the FastTree program as present in the folders "treeJTT", "treeWAG".
Resources
| Name |
Format |
Description |
Link |
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0 |
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http://data.europa.eu/88u/dataset/oai-zenodo-org-345101 |
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0 |
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http://data.europa.eu/88u/dataset/oai-zenodo-org-345101 |
Tags
- stramenopiles
- phylogenomics
- diatom
- pseudo-nitzschia-multistriata
- phylogenetic-trees