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罗布兰夫 / sarscov2phylo:20-10-20

罗布兰夫; 理查德·曼斯菲尔德


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    <dct:title>roblanf / sarscov2phylo:20-10-20</dct:title>
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    <dct:description>Citation and reuse &lt;p&gt;Please cite this release as:&lt;/p&gt; &lt;blockquote&gt;&lt;p&gt;Lanfear, Rob (2020). A global phylogeny of SARS-CoV-2 sequences from GISAID. Zenodo 土井: 10.5281 / zenodo.3958883&lt;/p&gt; &lt;/blockquote&gt; &lt;p&gt;You can visit that 土井 here: &lt;a href="//americinnmankato.com/badge/latestdoi/260124648"&gt;&lt;/a&gt;&lt;/p&gt; &lt;p&gt;If you publish papers that use this tree you must still follow the GISAID data sharing and attribution rules.&lt;/p&gt; Details &lt;p&gt;The trees in this release were generated with the following command line:&lt;/p&gt; &lt;p&gt;&lt;code&gt;bash global_tree_gisaid_start_tree.sh -i [gisaid.fasta] -p [previous_iteration] -t 250&lt;/code&gt;&lt;/p&gt; &lt;ul&gt; &lt;li&gt;&lt;p&gt;[gisaid.fasta] is the fasta file of high coverage and complete raw sequences from GISAID up to and including the date in the title of the release, determined by the 'submission date' filter on a GISAID data feed&lt;/p&gt; &lt;/li&gt; &lt;li&gt;&lt;p&gt;[previous_iteration] is the filepath of the previous release, this is used to provide the &lt;code&gt;excluded_sequences.tsv&lt;/code&gt; and &lt;code&gt;ft_SH.tree&lt;/code&gt; files as the starting points of the current iteration.&lt;/p&gt; &lt;/li&gt; &lt;/ul&gt; Filtering statistics &lt;pre&gt;&lt;code&gt;sequences downloaded from GISAID 115915 // alignment stats of global alignment Alignment number: 1 Format: aligned FASTA Number of sequences: 113964 Alignment length: 29903 Total # residues: 3396458802 Smallest: 29030 Largest: 29903 Average length: 29802.9 Average identity: 100% // alignment stats of global alignment after masking sites Alignment number: 1 Format: aligned FASTA Number of sequences: 113964 Alignment length: 29903 Total # residues: 3380968354 Smallest: 28961 Largest: 29675 Average length: 29667.0 Average identity: 100% // alignment stats after filtering out short/ambiguous sequences Alignment number: 1 Format: aligned FASTA Number of sequences: 113773 Alignment length: 29903 Total # residues: 3375311628 Smallest: 28961 Largest: 29675 Average length: 29667.1 Average identity: 100% // alignment stats of global alignment after trimming sites that are &amp;gt;50% gaps Alignment number: 1 Format: aligned FASTA Number of sequences: 113773 Alignment length: 29646 Total # residues: 3366377155 Smallest: 28437 Largest: 29646 Average length: 29588.5 Average identity: 100% // After filtering sequences with TreeShrink Type: Phylogram #nodes: 198720 #leaves: 113615 #dichotomies: 80830 #leaf labels: 113615 #inner labels: 75972 Number of new sequences added this iteration 398 alignment_names_new.txt &lt;/code&gt;&lt;/pre&gt; Notable changes to the scripts in this release &lt;ul&gt; &lt;li&gt;Scripts have changed to include some simple QC.&lt;/li&gt; &lt;/ul&gt; Notable aspects of the trees &lt;ul&gt; &lt;li&gt;None&lt;/li&gt; &lt;/ul&gt;</dct:description>
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