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Description
The dataset contains alignment and consensus matrix files, and results of phylogenetic analysis of ITS1- 5,8S-ITS2 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)
The ITS matrix consisted of 814 features.433 features were parsimonically informative, 90 features were non-informative, and 291 belonged to constant features. The MP method generated over 10,000 trees with a length of 3045; CI 0.49; RI 0.631. The ratio of transition to transversion was 1.81.
Sequences had to be edited in the FinchTV program, and then two complementary threads ( „forward” and „reverse” ) of each taxon were combined into one consensus thread in the AutoAssembler program and then a matrix with data was created. With the help of the ClustalX sequences were pre-matched, and then the correction was made in the 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 - Raw data:
- Data contained in dataset was not processed.
Details
- Year of publication:
- 2024
- Verification date:
- 2024-04-30
- Dataset language:
- English
- Fields of science:
-
- biological sciences (Natural sciences)
- DOI:
- DOI ID 10.34808/dcqb-np54 open in new tab
- Verified by:
- Gdańsk University of Technology
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