Supporting data for the paper "CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments"
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| author | Ponty, Yann Los Alamos National Laboratory European Molecular Biology Laboratory - European Bioinformatics Institute |
| author_facet | Ponty, Yann Los Alamos National Laboratory European Molecular Biology Laboratory - European Bioinformatics Institute |
| contents | <div> <p>Four files used in the paper “CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments” are made available here for reproducibility:</p> <ul> <li><code>random_datasets_len10000_num30000.zip</code> : An archive of artificial FASTA files generated as described in the paper.</li> <li><code>HIV1_ALL_2022_genome_DNA.fasta.xz</code> : A multiple sequence alignment of 5,381 HIV1 genomes, <a href="https://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html">retrieved from the Los Alamos National Laboratory</a> on March 2025.</li> <li><code>nextstrain_groups_LANL-HIV-DB_HIV_genome_timetree.jsonl.gz</code> : A JSONL file, as produced by <a href="https://nextstrain.org/groups/LANL-HIV-DB/HIV/genome">Nextstrain</a>, of the phylogeny of 3,090 HIV genomes among the 5,381 from the previous file. </li> <li><code>MFS_1.fasta.xz</code> : A multiple sequence alignment of 214,283 protein sequences of the Major Facilitator Superfamily (MFS), <a href="https://www.ebi.ac.uk/interpro/download/pfam/">retrieved from Pfam</a> on March 2025.</li> </ul> </div> |
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| publishDate | 2025 |
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| spellingShingle | Supporting data for the paper "CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments" Ponty, Yann Los Alamos National Laboratory European Molecular Biology Laboratory - European Bioinformatics Institute <div> <p>Four files used in the paper “CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments” are made available here for reproducibility:</p> <ul> <li><code>random_datasets_len10000_num30000.zip</code> : An archive of artificial FASTA files generated as described in the paper.</li> <li><code>HIV1_ALL_2022_genome_DNA.fasta.xz</code> : A multiple sequence alignment of 5,381 HIV1 genomes, <a href="https://www.hiv.lanl.gov/content/sequence/NEWALIGN/align.html">retrieved from the Los Alamos National Laboratory</a> on March 2025.</li> <li><code>nextstrain_groups_LANL-HIV-DB_HIV_genome_timetree.jsonl.gz</code> : A JSONL file, as produced by <a href="https://nextstrain.org/groups/LANL-HIV-DB/HIV/genome">Nextstrain</a>, of the phylogeny of 3,090 HIV genomes among the 5,381 from the previous file. </li> <li><code>MFS_1.fasta.xz</code> : A multiple sequence alignment of 214,283 protein sequences of the Major Facilitator Superfamily (MFS), <a href="https://www.ebi.ac.uk/interpro/download/pfam/">retrieved from Pfam</a> on March 2025.</li> </ul> </div> |
| title | Supporting data for the paper "CREMSA: Compressed Indexing of (Ultra) Large Multiple Sequence Alignments" |
| url | https://doi.org/10.5281/zenodo.15100011 |