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Description
The dataset contains alignment and consensus matrix files, and results of phylogenetic analysis of plastid matK region from 186 orchid species considered to belong Oncidieae subtribe. Sequences were assessed from NCBI GeneBank (list of all records with identifiers in the separate file)
In the parsimony (MP) analysis, a matrix consisting of 1359 features was used, of which 358 were parsimonically informative, 198 were non-informative, and 803 were constant features. The MP method generated more than 10,000 trees with a length of 1464; CI 0.505, RI 0.714. The ratio of transition to transversion was 0.59.
Sequences had to be edited in the FinchTV program, and then combine two complementary threads ( „forward” and „reverse” ) of each taxon into one consensus thread in the AutoAssembler program and then a matrix with data was created. With the help of the program „ClustalX” sequences were pre-matched, then the correction was made in the program Seaview. For phylogenetic analysis, the parsimony method based on features (MP – maximum parsimony) was used. The Fitch algorithm was used to calculate the number of evolutionary changes, and the nonparametric bootstrap method was used to estimate the reliability of individual phylogenetic tree clades (1000 repeats; 50%).
Dataset file
hexmd5(md5(part1)+md5(part2)+...)-{parts_count} where a single part of the file is 512 MB in size.Example script for calculation:
https://github.com/antespi/s3md5
File details
- License:
-
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CC 0Public Domain Dedication
Details
- Year of publication:
- 2024
- Verification date:
- 2024-04-30
- Dataset language:
- English
- Fields of science:
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- biological sciences (Natural sciences)
- DOI:
- DOI ID 10.34808/p8y1-m788 open in new tab
- Verified by:
- Gdańsk University of Technology
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