Phylogenetic datasets for Phaeodactylum MCFc (Giustini et al. 2025)
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Phylogenetic datasets for Phaeodactylum MCFc (Giustini et al. 2025)DescriptionArchive containing alignments in FASTA format (before and after <code>ali2phylip.pl</code>) and trees built with <code>IQ-TREE 2</code> in Newick format for the different stages of the analysis:OG0001460-FigA:orthogroup before enrichmentremoved sequences: Monosiga and PorphyraOG0001460-8-raw:orthogroup after enrichmentOG0001460-8-FigB:orthogroup after enrichmentremoved sequences: Bolidomonas ans PavlovaOG0001460-8-FigC:orthogroup after enrichmentremoved sequences: Ochropytes-specific gene copy (and Bolidomonas)Files in archive:<pre><pre>.<br>├── OG0001460-8-FigB-a2p.fasta<br>├── OG0001460-8-FigB.fasta<br>├── OG0001460-8-FigB.tre<br>├── OG0001460-8-FigC-a2p.fasta<br>├── OG0001460-8-FigC.fasta<br>├── OG0001460-8-FigC.tre<br>├── OG0001460-8-raw-a2p.fasta<br>├── OG0001460-8-raw.fasta<br>├── OG0001460-8-raw.tre<br>├── OG0001460-FigA-a2p.fasta<br>├── OG0001460-FigA.fasta<br>├── OG0001460-FigA.tre<br>└── README.md</pre></pre>CommandsAlignment filtering<pre><pre>ali2phylip.pl --p80 --min=0.5 --max=0.5 –map-ids OG0001460-8-raw.fasta</pre></pre>Tree inference<pre><pre>iqtree2 -bb 1000 -m C20 -s OG0001460-8-raw.p80</pre></pre>Tree formatting<pre><pre>format-tree.pl --map-ids --itol --ladderize=asc --annotate='no rank' \<br> --collapse=color --colorize=klepto-cb.cls --taxdir=taxdump-20230504/ \<br> --in=.p80 --out=-C20 --root-on-family=outg OG0001460-8-raw.p80.treefile<br></pre></pre>
提供机构：
figshare
创建时间：
2025-01-14
