ecthomson/AFI
(2024).
ecthomson/AFI.
[Dataset].
Github.
https://github.com/ecthomson/AFI/
Multiple sequence alignments and phylogenetic trees for AFI study Emma Thomson and Shirin Ashraf 30/12/2024 Multiple sequence alignments were generated using MAFFT v7.487 with local alignment and 1000 iterations. Maximum-likelihood phylogenetic analysis was carried out for viruses with at least 10 percent genome coverage using IQ-TREE multicore version 1.6.12 and with 1000 ultra-fast bootstrap replicates using relevant reference sequences. Substitution models mentioned in figure legends were best fit models as reported by IQ-TREE. Uncorrected pairwise-distances were estimated using MEGA 10.0. Sequence read data is available under Bioproject PRJNA1143542.
Keywords
Phylogenetic analysis| Item Type | Dataset |
|---|---|
| Resource Type |
Resource Type Resource Description Dataset Quantitative |
| Capture method | Other |
| Date | 30 December 2024 |
| Language(s) of written materials | English |
| Creator(s) |
Thomson, EC
|
| LSHTM Faculty/Department | Faculty of Infectious and Tropical Diseases > Dept of Clinical Research |
| Participating Institutions | London School of Hygiene & Tropical Medicine, London, United Kingdom |
| Date Deposited | 03 Apr 2025 08:47 |
| Last Modified | 22 Jul 2025 15:29 |
| Publisher | Github |
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