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README.md

Analysis Description

Use a partition annotation file, and a time-scaled MCC tree, split the alignment into partitions, fit partition-specific models with substitution rates partitioned into terminal and interior nodes, report the MLEs

  • Citation: "Combining chemical and evolutionary information to effectively evaluate HIV and SIV genetic heterogeneity and RNA structural conservation within and among infected hosts", by Rife et. al.

  • Written by: Sergei L Kosakovsky Pond

  • Contact Information: [email protected]

  • Analysis Version: 1.00

How to run

  1. Download and install HyPhy (www.hyphy.org). This script is confirmed to work with v2.3.3 (https://github.com/veg/hyphy/releases/tag/v2.3.3), but may also work with newer versions
  2. Run fit-nexus-partitions.bf in HyPhy, e.g. $HYPHYMP /path/to/fit-nexus-partitions.bf
  3. When prompted,
    • supply the name of the NEXUS file with partitions specified as CHARSET blocks (see data/N01.nex for an example)
    • Agree to use the tree in the file or specify a separate tree (in Newick format with branch lengths in units of time)
  4. Output is written to standard out as a Markdown text

Example output

Loaded an MSA with 443 sequences and 1308 sites from /Volumes/sergei-raid/Coding/pubs/HIV-RNA/hyphy-2.3.3/../data/N01.nex

Read 10 partitions on 1308 sites.

Fitting partition CODON1+2 with 358 constant sites, 94 variable sites, and 47 phylogenetically informative sites

  • log (L) -3476.108
  • π (A) 0.232
  • π (C) 0.228
  • π (G) 0.292
  • π (T) 0.248
  • Internal node rate 0.0000176 [0.0000150 - 0.0000208]
  • Internal node kappa 5.863 [4.710 - 7.210]

Fitting partition CODON3 with 126 constant sites, 111 variable sites, and 58 phylogenetically informative sites

  • log (L) -3078.507
  • π (A) 0.212
  • π (C) 0.195
  • π (G) 0.266
  • π (T) 0.326
  • Internal node rate 0.0000330 [0.0000272 - 0.0000390]
  • Internal node kappa 7.140 [5.746 - 8.747]

Fitting partition CODON4+5 with 310 constant sites, 108 variable sites, and 48 phylogenetically informative sites

  • log (L) -2952.911
  • π (A) 0.538
  • π (C) 0.107
  • π (G) 0.161
  • π (T) 0.194
  • Internal node rate 0.0000138 [0.0000114 - 0.0000175]
  • Internal node kappa 4.997 [3.846 - 6.381]

Fitting partition CODON6 with 116 constant sites, 79 variable sites, and 47 phylogenetically informative sites

  • log (L) -2602.324
  • π (A) 0.384
  • π (C) 0.111
  • π (G) 0.130
  • π (T) 0.375
  • Internal node rate 0.0000335 [0.0000289 - 0.0000383]
  • Internal node kappa 32.190 [26.282 - 40.115]