@@ -13,19 +13,14 @@ following results:
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- a multiple sequence alignment of high-quality consensus sequences
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for each time point
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-
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- a maximum-likelihood phylogenetic tree, inferred using
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[ FastTree] ( http://www.microbesonline.org/fasttree/ )
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-
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- the most recent common ancestor (MRCA) and other inferred ancestor
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sequences
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-
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- a two-dimensional embedding that respects TN93 sequence distances
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-
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- per-site selection pressure, inferred using
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[ FUBAR] ( https://veg.github.io/hyphy-site/methods/selection-methods/ ) ,
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and other per-site evolutionary metrics
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-
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- per-segment evolutionary and phenotypic metrics, inferred using
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[ HyPhy] ( http://www.hyphy.org/ )
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@@ -34,6 +29,11 @@ The pipeline logic is implemented in
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pipeline has been submitted for publication. A link to the journal
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article will be added here when it is available.
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+ See also:
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+
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+ - [ flea-server] ( https://github.com/veg/flea-server )
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+ - [ flea-web-app] ( https://github.com/veg/flea-web-app )
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+
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Setup
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=====
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@@ -108,7 +108,10 @@ steps. The two files that contain the final results are:
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- ` session.json ` : a JSON file to be visualized with
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[ ` flea-web-app ` ] ( https://github.com/veg/flea-web-app ) .
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-
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- ` session.zip ` : a zip file with FASTA files for the consensus
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sequences, ancestors, and MRCA, and a Newick file containing the
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- rooted phylogenetic tree.
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+ rooted phylogenetic tree.
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+
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+ These files can be served with
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+ [ flea-server] ( https://github.com/veg/flea-server ) and visualized with
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+ [ flea-web-app] ( https://github.com/veg/flea-web-app ) .
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