spond

{
 "analysis":{
   "authors":"Sergei L Kosakovsky Pond, Ben Murrell, Steven Weaver and Temple iGEM / UCSD viral evolution group",
   "citation":"Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection (2015). Mol Biol Evol 32 (5): 1342-1353. v2.2 adds support for multiple-hit models",
   "contact":"spond@temple.edu",
   "info":"aBSREL (Adaptive branch-site random effects likelihood)\n                            uses an adaptive random effects branch-site model framework\n                            to test whether each branch has evolved under positive selection,\n                            using a procedure which infers an optimal number of rate categories per branch.",
   "requirements":"in-frame codon alignment and a phylogenetic tree",
   "version":"2.2"
  },
 "branch attributes":{

spond

A hackish example for annotating trees

This example uses tree.style_nodes to append colored rectangles to the node names as annotations. It requires some less than pretty spacing calculations in the handler, but both radial and rectangular layouts are supported.

This is in reference to veg/phylotree.js#64

spond

A JavaScript simulation of within host HIV dynamics

This code is based off a Python script kindly provided by Daniel Rosenbloom.

To INSTALL and RUN you need to have node.js and npm on your system

INSTALL and RUN

$git clone https://gist.github.com/spond/417b66f99731142268bacd957b752b09 HIV-sim

spond

How to add custom context menu items to tree nodes

This is accomplished via a call to d3_add_custom_menu which adds a menu to a specific node with callback defining

1. What text is displayed (based on the node object and associated data)
2. What happens on click (pass nodes and other data through transitive closure, because standard d3 .on handlers will be called on the menu item, not the node object).
3. When the menu item is shown (a boolean callback based on the node object and associated data)

spond

Compare the results of MEME and MEME-internal on the same dataset

The table shows any site which was found significant (p ≤ 0.05) by either version of MEME.

spond

Compare the results of MEME and MEME-internal on the same dataset

The two charts show mean ω (internal branches only, for MEME-internal, and the entire tree for MEME) over sites. Sites with evidence for episodic diversifying selection are shown as circles along the x-axis.

spond

Root-to-tip regression for intrahost HIV-1 phylogenies.

In this example, we read in trees with branch lengths (FastTree2), based on haplotypes and counts reported in Lorenzo-Redondo et al, construct root-to-tip distances for time-stamped tips, and regress those on time to obtain crude evolutionary rate estimates.

The initial rooting of the tree is obtained by considering all time-point 0 sequences and selecting one that maximizes R² (regardless of the slope). The user can perform arbitrary rerooting and see what the effect on the regression slope is.

Further, 1000 simulated perturbation of haplotype counts are considered for a given rooting: the estimated frequency of each haplotype (encoded in the tip name) is multiplied by a random number from [0.05-10] distributed uniformly. The proportion of perturbations with positive inferred regression slopes is shown on the chart.

spond

Plot site-by-site estimates of dN-dS from FUBAR .csv files

Take the output (main .CSV) of FUBAR, and create a D3 plot over sites. Optionally, partition the plot into chunks of different color (e.g. gene/genome regions), and annotate them with horizontal bars.

spond

Annotated tree

An example that shows how to use styling call-backs to

1. Color terminal branches based on an externally supplied annotation (cluster assignment)
2. Adjust thickness of interior branches based on their bootstrap support
3. Label interior nodes (for the cladogram layout) with bootstrap values

spond

Within-host HIV tree.

This is an example which parses leaf names for meta information, including compartment, sample date, and copy number, and then annotates the tree accordingly. This example demonstrates how to use styling callbacks, e.g. style_nodes, and node_span.

The example also uses Bootstrap to allow interactive tree input via a model dialog.

More documentation forthcoming.