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| Main Author: | |
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| Format: | Recurso digital |
| Language: | English |
| Published: |
Zenodo
2026
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| Subjects: | |
| Online Access: | https://doi.org/10.5281/zenodo.20110751 |
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Table of Contents:
- <p>The <a href="https://doi.org/10.1101/2024.11.30.626202" rel="noopener">minimum evolution with the molecular clock (MEMC) guide tree</a> for multiple sequence alignment (MSA).</p> <p>This is <a href="https://www.lbgi.fr/balibase/BalibaseDownload/BAliBASE_R1-5.tar.gz" rel="noopener">BAliBASE 3.0</a> benchmark test results using <a href="https://gitlab.com/sysimm/mafft/-/tree/ee9799916df6a5d5103d46d54933f8eb6d28e244" rel="noopener">MAFFT (ver. 7.526)</a>.</p> <p>The data includes the following:</p> <p>1. bb3_release: BAliBASE 3.0 benchmark</p> <p>2. data_gen_codes: Codes used for generating the data. Each folder corresponds to each subsection in the Results of our paper.</p> <p>3. dm_l_ins: Contains two folders (l_ins_dm_hat2 in .hat2 format, l_ins_dm_txt in .txt format) for distance matrices.</p> <p>4. mafft_gt: Contains 13 different guide trees generated using 11 different algorithms based on the same distance matrices in dm_l_ins. A folder named "memc_bqm", "memc_con", "memc_nl" includes guide trees generated by our algorithm. The source code for MEMC guide trees is available in the <a href="https://github.com/Bevacizumab/memcguidetree" rel="noopener">GitHub repository</a>.</p> <p>5. mafft_msa: MSA results generated using MAFFT and the guide trees from mafft_gt. The numbers at the ends of the folder names (0, 1, 2, 1000) represent maxiterate in MAFFT command.</p> <p>6. mafft_msa_reorder: For computing BAliBASE scores, the MSA results should be reordered.</p> <p>7. mafft_msa_score: BAliBASE 3.0 benchmark scores for the MSA results (<a href="https://github.com/robinhundt/bali-score">link</a>).</p> <p>8. tsp_order: Contains solutions (in .txt format) to the traveling salesperson problems used for constructing the MEMC guide tress. We used Concorde, the D-Wave BQM solver, and the D-Wave NL solver (with full-sample outputs).</p>