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Cultivate your MSA to get better trees

Project description

Arbow: cultivate your multiple sequence aligment to get better trees

Name

We called arbow as that would be the phonetic pronounciation of the short, endearing, terms for an arborist in Australia.

What it does

The goal of arbow is to automate and simplify the production of trees from multiple sequence alignments.

In this version it does:

  1. Reads all the alignment
  2. Calculates stats per column in the alignment
  3. Allows the user to set a threshold of tolerable missing data in a column, and arbow removes all non-conforming columns from the alignment
  4. From the remaining columns, arbow finds all the constant columns, and calculates the frequency of A, C, G, and T.
  5. It then filters out all the variable columns, and outputs that as a multiFASTA alignment.
  6. It runs IQTree with a few sensible presets

Currently, in step 4 above, columns that have a single base but still have missing data that did were not filtered out in step 3 are counted as being the base. In other words, if a user specifies a maximum number of 20 missing bases, and a column with 5 missing bases but with A in all samples, it will count towards A (i.e., majority consensus imputation).

For step 5, missing data (i.e., - and N) are all codes as N.

Tests are underway to figure out how these assumptions might affect the output.

Dependencies

  1. Python >=3.6
  2. IQTree 1.6+ (not tested on IQTree 2 as it is not production ready yet)
  3. BioPython
  4. Pandas
  5. NumPy

Installation

Brew

brew install iqtree
pip<3> install arbow

Conda

conda install -c bioconda iqtree
pip<3> install arbow

Running

  1. Generate a mulitple sequence alignment with your favourite aligner (e.g., MAFTT). Output a multiFASTA file.
  2. Run arbow <aln.fa>
  3. Open tree-YYYY-MM-DD_HHMMSS.treefile in your favourite tree viewer (e.g, FigTree)

Data stream

When running arbow, by default a stream is output to the console (stdout).

Data about the each sequence in the alignment is prefixed with [SEQ], and is followed by:

  1. Count of each base (A, C, G, T, and NN is any character other than ACGT)
  2. Percent missing data
  3. A status column that has 0, 1, 2, or 3 * depending on whether the percent missing data is <0.5, >=0.5 and <1.0, >=1.0 and <5.0, or >=5.

Data about each column in the alignment is prefixed with [ALN], and is followed by:

  1. Position in the alignment
  2. Count of each base (bases counted will depend on whether all IUPAC codes are allowed or not - see below in usage)

Command line

Usage

Usage: arbow [OPTIONS] ALN

Options:
  --version
  -a, --all-iupac               Print count of all IUPAC code for column
                                stats?

  -s, --no-stream               Stop streaming stats to console
  -mm, --max-missing INTEGER    Remove sites with 'mm' missing sites or more
                                [default: 20]

  -o, --out-var-aln TEXT        Filename for alignment of variable sites.
                                [default: aln-2020-04-07-150443.aln]

  -p, --prefix TEXT             Prefix to append to IQTree output files.
                                [default: tree-2020-04-07-150443]

  -t, --iqtree-threads INTEGER  Number of cores to run IQtree  [default: 4]
  -m, --iqtree-models TEXT      Substitution models to test.  [default:
                                HKY,TIM2,GTR]

  -f, --iqtree-freq TEXT        Base frequency models to test.  [default: F]
  -r, --iqtree-rates TEXT       Rate category models to test.  [default: G,R]
  -b, --iqtree-bb INTEGER       Maximum number of UltraFast Bootstrap
                                iterations to attempt.  [default: 1000]

  -a, --iqtree-alrt INTEGER     Number of replicates to perform SH-aLRT.
                                [default: 1000]

  -c, --iqtree-cmax INTEGER     Maximum number of rate categories to test.
                                [default: 5]

  --help                        Show this message and exit.

Get help

arbow --help

Get version

arbow --version

Project details


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