https://github.com/nylander/likelihood-mapping-with-iqtree
Likelihood-mapping in iqtree2
https://github.com/nylander/likelihood-mapping-with-iqtree
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Likelihood-mapping in iqtree2
- Host: GitHub
- URL: https://github.com/nylander/likelihood-mapping-with-iqtree
- Owner: nylander
- License: mit
- Created: 2021-11-11T17:06:04.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2024-12-20T12:15:39.000Z (over 1 year ago)
- Last Synced: 2024-12-20T13:26:33.487Z (over 1 year ago)
- Language: Shell
- Size: 258 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Likelihood mapping with iqtree2
- Last modified: fre dec 20, 2024 12:10
- Sign: Johan Nylander
## Description
Script for running likelihood mapping (Strimmer & von Haeseler, 1997) with
iqtree2 (Minh et al., 2020), and summarize the run as the fraction of highly
supported quartets for the data.
Reads a fasta-formatted input file (multiple sequence alignment) as input,
prints the fraction of "highly supportive" quartets as output (to file or
stdout, or both).
## Installation
The script is written in bash, and requires `iqtree2` (www.iqtree.org) to be installed.
The full path to `iqtree2` can changed directly in the script (line 14) if needed.
In order to utilize all functionality of the provided `Makefile`, GNU make and
GNU parallel needs to be installed.
If `make` is installed, the script can be installed (in `/usr/local/bin`) by using
$ make install
To install in another location, e.g., `$HOME/bin`, use
$ make PREFIX=$HOME install
## Usage
$ run_iqtree_lmap.sh [-n 10000][-a 50][-m TEST][-t AUTO][-c 0.70][-d][-x][-q][-v][-h] infile.fasta
### Options
-n number -- Specify the number of quartets to be sampled. Default
is using a multiplier on the number of sequences in the
infile (see option -a).
-a number -- Specify the multiplier to use for automatically set the
number of quartets sampled. The total number of quartets
are number of sequences times the multiplier.
Default multiplier is 50.
-m model -- Specify the model to use. Default is TEST.
-t number -- Specify number of threads for iqtree2. Default is 'AUTO'.
-c cutoff -- Specify a cutoff-level (0-1) for files to be reported.
If the fraction of supported quartets are below this value,
the file name is printed. Default is to print output for all
files.
-d -- Do not parse the output (the .lmap.quartetlh file).
-x -- Remove all iqtree2 output except the .lmap.quartetlh file.
Default is to keep all files.
-q -- Be quiet (noverbose)
-v -- Print version.
-h -- Print help message.
### Examples
$ run_iqtree_lmap.sh infile.fasta
$ run_iqtree_lmap.sh -d -x infile.fasta
$ run_iqtree_lmap.sh -a 25 -c 0.80 -m 'GTR+G4' -t 10 -x -q infile.fasta
### Input
Fasta formatted sequence files (aligned, that is, all sequence entries
should be of the same length).
### Output
The name of the input file and the corresponding fraction of highly supported
quartets are written to a .lmap.out file.
The .lmap.quartetlh from iqtree2 will also be kept (other files from iqtree2
can be removed using `-x`).
If the `-c` option is used, the file name of the files not matching the cutoff
standard will be printed to stdout. This list can then be captured in downstream
steps.
## License
Copyright (C) 2021-2025 Johan Nylander
Distributed under terms of the [MIT license](LICENSE).
## Likelihood mapping run manually
### 1. Run iqtree2
$ iqtree2 -s data/infile.fasta -lmap ALL -wql -n 0 -m TEST
The `data/infile.fasta.lmap.quartetlh` file -- an example (first two lines):
SeqIDs lh1 lh2 lh3 weight1 weight2 weight3 area corner
(8,3,17,16) -7456.47 -7532 -7522.94 1 0 0 1 1
- lh1 is the log-likelihood of the quartet tree {8,3} | {17,16}
- lh2 is the log-likelihood of the quartet tree {8,17} | {3,16}
- lh3 is the log-likelihood of the quartet tree {8,16} | {3,17}
- weight1 = exp(lh1) / (exp(lh1)+exp(lh2)+exp(lh3))
- weight2 = exp(lh2) / (exp(lh1)+exp(lh2)+exp(lh3))
- weight3 = exp(lh3) / (exp(lh1)+exp(lh2)+exp(lh3))
- (That means, they are the likelihood weights of the 3 quartets).
### 2. Parse the `.lmap.quartetlh` file to give proportion of well-supported quartets
That is, count the number of times a quartet ends up in any of the "corner"
areas 1, 2, or 3, over the total number of sampled quartets.
$ awk 'BEGIN{i=0}!/SeqIDs/{i=i+1; if($8==1||$8==2||$8==3) a=a+1}END{print a/i}' data/infile.fasta.lmap.quartetlh
## Try also
If you have several fasta files and a multi-core computer, you may also try to
run the likelihood mapping in parallel (by utilizing the provided
[`Makefile`](Makefile) and `data` folder).
1. Make sure you have `iqtree2`, `make`, and `parallel` (GNU parallel)
installed
2. Put your fasta-formatted alignments (files ending in `.fas`) in the `data`
folder
4. Run
$ make run > lmap.out &
## Links and further reading
- [Minh et al. 2020](https://academic.oup.com/mbe/article/37/5/1530/5721363)
- [Strimmer and von Haeseler 1997](doc/Strimmer_von_Haeseler_1997.pdf)
- [igtree2, www.iqtree.org](http://www.iqtree.org)
- [Likelihood-mapping in iqtree2, www.iqtree.org/doc/Command-Reference#likelihood-mapping-analysis](http://www.iqtree.org/doc/Command-Reference#likelihood-mapping-analysis)
- [Post on google groups, groups.google.com/g/iqtree/c/OcfgC0RF110](https://groups.google.com/g/iqtree/c/OcfgC0RF110)
- [GNU parallel, www.gnu.org/software/parallel](https://www.gnu.org/software/parallel/)
- [GNU make, www.gnu.org/software/make](https://www.gnu.org/software/make/)