PHYLOTYPER

Phylotyper predicts biological subtypes from gene sequence data. It build a reference phylogenetic tree from genes with known subtype and then uses ancestral reconstruction to assign likelihoods of each subtype to the branch points in the tree. A new unknown sequence can be assigned a subtype based on the extrapolated value from its ancestors in the tree.

https://github.com/superphy/insilico-subtyping

CONTENTS

1. Examples
2. Installation
3. Running Phylotyper
   1. Setting up Phylotyper config file
   2. Running Phylotyper using built-in subtype scheme
   3. Built-in subtype schemes
   4. Adding new subtype scheme to Phylotyper
4. [Contributing to Phylotyper]((#contributing-to-phylotyper)
5. About Phylotyper
6. Contact

EXAMPLES

The following instructions provide a quick demonstration of Phylotypers functions. After installing phylotyper and its dependencies, switch into the Phylotyper source directory (if following the Installation Instructions for pip in this document, this location would be phylotypervm/src/phylotyper/).

1. Inform phylotyper of the locations for non-default dependencies by setting up a INI config file

Details here.

2. Predict a subtype for one of the amino acid schemes packaged in phylotyper:

   phylotyper genome stx2 example_data/output/ example_data/genome.fasta --config yourconfigfile.ini

See example_data/output/ for the results. Find the full list of available schemes and their sequence types here. Details on the results can be found here. Note: the config file can also be specified using the enviromentment variable PHYLOTYPER_CONFIG instead of the --config option.

3. Add your own DNA subtype scheme called myexample:

   phylotyper new myexample example_data/example_subtypes.tsv example_data/output3/ \ example_data/dna_example_genes.fasta --config yourconfigfile.ini

Note: that this scheme has a low prediction F1-score. Compare this score to the 2-loci amino acid value in step 5. Using amino acid vs. DNA sequences or multiple vs single loci can alter the performance when the associated phylogenetic tree does better or worse at separating subtypes.

4. Use this new DNA subtype scheme to predict subtypes:

   PHYLOTYPER_CONFIG=yourconfigfile.ini phylotyper genome myexample example_data/output4/ example_data/genome.fasta

See example_data/output4/ for the results. Details on the results can be found here.

5. Add your own multi-loci amino acid subtype scheme called myexample2:

   phylotyper new myexample2 example_data/example_subtypes.tsv example_data/output5/ \ example_data/aa_example_genes_loci1.fasta example_data/aa_example_genes_loci2.fasta --aa \ --config yourconfigfile.ini

6. Use this new amino-acid subtype scheme to predict subtypes:

   phylotyper genome myexample2 example_data/output6/ example_data/genome.fasta --config yourconfigfile.ini

See example_data/output6/ for the results.

INSTALLATION

Phylotyper is a python package that uses several external programs. Phylotyper requires the following external programs:

1. FastTree (tested with version 2.1) - http://www.microbesonline.org/fasttree/
2. MAFFT (tested with version 7.1) - http://mafft.cbrc.jp/alignment/software/
3. trimAI (tested with version 1.2) - http://trimal.cgenomics.org/
4. BLAST+ (tested with version 2.2.28) - ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
5. R (tested with version 3.3.2) - https://cran.r-project.org/

Phylotyper was built and tested with python 2.7.

There are two ways to install Phylotyper 1) with pip, external programs are installed by user or 2) with conda and all external programs are automatically installed via conda

1. To install Phylotyper using pip in a python virtual environment:

• virtualenv -p python2.7 phylotypervm. Install virtual environment.
• source phylotypervm/bin/activate. Activate the virtual enviroment.
• pip install -e git+https://github.com/superphy/insilico-subtyping.git#egg=Phylotyper. Install Phylotyper.
• If external programs are not available in the Linux search path, they need to be defined using a config file. See section Setting up Phylotyper config file

2. To install Phylotyper and external programs in a conda environment:

• conda create --name phylotyper. Create environment.
• source activate phylotyper. Activate environment.
• conda install -c mdwhitesi phylotyper. Install Phylotyper and dependencies in environment.

RUNNING PHYLOTYPER

Setting up Phylotyper config file

Phylotyper has user-defined settings and also requires several external programs. If external programs are not available in the Linux search path, the location of the executable can be provided to Phylotyper through a INI-config file. Also if you wish to override the default for probability cutoff of 0.9 for assigning subtypes, you can do this in the config file. The config file can contain the following settings:

; Sample Phylotyper config file
;

# External programs
[external]
fasttree=/path/to/FastTree
mafft=/path/to/mafft
trimal=/path/to/trimal
makeblastdb=/path/to/makeblastdb ; part of the BLAST+ suite
blastn=/path/to/blastn ; part of the BLAST+ suite
blastx=/path/to/blastx ; part of the BLAST+ suite
blastdbcmd=/path/to/blastdbcmd ; part of the BLAST+ suite

# R settings
[R]
lib=/path/to/local/R/libs/ ; Location where downloaed R packages can be saved
repo=http://cran.stat.sfu.ca/ ; HTTP address of R repository to use for downloading R packages
rscript=/usr/bin/Rscript ; Part of the R suite

# Phylotyper settings
[phylotyper]
prediction_threshold=0.9 ; Cutoff for calling subtype assignments

Set up environment variable export PHYLOTYPER_CONFIG=/path/to/your/phylotyper/config/file to indicate location of config file to Phylotyper. To make this variable persistent, the line export PHYLOTYPER_CONFIG=/path/to/your/phylotyper/config/file can be added to your ~/.bashrc.

Alternatively, the location of the config file can be set using the argument --config when running phylotyper.

Running Phylotyper using built-in subtype scheme

See section Setting up Phylotyper config file.

Phylotyper can first identify putative subtype loci in input genomes and then use the detected loci to predict subtypes. To run phylotyper with genome DNA sequences as input:

phylotyper genome subtype_scheme output_directory genome_input1.fasta [genome_input2.fasta genome_input3.fasta...][--noplots][--config /path/to/config/file][--index /path/to/index/file]

Arguments:

1. genome - Sub-command for running phylotyper on genome input. Other sub-commands are new for building new subtype schemes.
2. subtype_scheme - The name for the subtype scheme. See Built-in subtype schemes for a list of the subtypes currently packaged with phylotyper. E.g. value stx2.
3. output_directory - Results and graphics will be output to this directory. Files will be overwritten.
4. genome_input1.fasta - Genome multi-fasta DNA sequence input. Multiple genomes should be provided as separate files.

Options:

1. --noplots - Turn off figures.
2. --config /path/to/file - Phylotyper config file. Can also be set in environment variable PHYLOTYPER_CONFIG. See Setting up Phylotyper config file.
3. --index /path/to/file - YAML-format file that lists the locations of subtype reference files. You can specify a file that is not the default file packaged with phylotyper.

Outputs:

The output directory is defined in the command-line arguments. The results of the phylotyper run is given in the file:

<output_directory>/subtype_predictions.tsv

This tab-delimited result file contains the following columns:

1. genome: Genome name
2. tree_label: Unique label for a given gene copy in a genome
3. subtype probability: The marginal likelihood from the Phylotyper analysis (or identical if an identical match was found in the reference set)
4. phylotyper_assignment: The subtype assignment provided that the probability is above the pre-defined cutoff
5. loci: A list of subtype genes found in the genome. Each list item contains a two-part tuple: 1. lcl|genome|unique_name followed by 2. lcl|genome|contig:start-stop.

Additional analysis files that are output include:

1. <genome>_loci<nloci>_step2_alignment_input.fasta Fasta-file containing subtype gene found in input genome by BLAST step. There can be multiple copies/alleles for a single gene loci (If there is only one genome and one loci, the file will be called '<input_filename>.locus1`)
2. <genome>_step3_alignment_trimming_summary.html HTML output from trimAI indicating trimmed columns in the alignment
3. <genome>_step4_profile_alignment_output.fasta Fasta-file containing aligned input genes and reference genes. MAFFT is used for the alignment.
4. <genome>_step5_subtype_tree.newick Newick-file containg phylogenetic tree. FastTree is used to build the tree.
5. <genome>_step5_posterior_probability_tree.png Image file showing the phylogenetic tree and marginal likelihoods for the unknown gene.

Built-in subtype schemes

Listed below are the subtypes, their sequence type, number of loci used in the prediction and a description of subtype. Inputs for genomes is always nucleotide multi-fasta sequences. Detected loci in genomes are translated if the subtype sequence type is amino acid. If the input are gene sequences, the correct sequence type and number of loci are required.

- stx1
..+ sequence type: nt
..+ number of loci: 2
..+ description: Escherichia coli Shiga-toxin 1 (Stx2) subtype
- stx2
..+ sequence type: aa
..+ number of loci: 2
..+ description: Escherichia coli Shiga-toxin 2 (Stx2) subtype
- eae
..+ sequence type: nt
..+ number of loci: 1
..+ description: Escherichia coli Initimin (eae) subtype
- wz
..+ sequence type: nt
..+ number of loci: 2
..+ description: Escherichia coli O-serotype based on wzy and wzx genes
- flic
..+ sequence type: nt
..+ number of loci: 1
..+ description: Escherichia coli H-serotype based on fliC gene

Adding new subtype scheme to Phylotyper

See section Setting up Phylotyper config file.

New subtype schemes can be added to phylotyper. The reference inputs will be processed and saved in the locations specified in the YAML-format file: subtypes_index.yaml. Optionally, you can define a non-default subtype data directory by providing your own YAML file using --index /path/to/index/file.

To create a new subtype for use in phylotyper:

phylotyper new subtype_scheme subtype_assignment_file output_directory reference_loci1.fasta [reference_loci2.fasta reference_loci3.fasta...][--aa][--config /path/to/config/file][--index /path/to/index/file][--description "Help description"]

Arguments:

1. new - Sub-command for adding new subtype in phylotyper. Other sub-commands are genome for running phylotyper on genome input.
2. subtype_scheme - The name for the subtype scheme.
3. subtype_assignment_file - Subtypes for input loci sequences. This is a tab-delimited file with genomes in column 1 and subtypes in column 2.
4. output_directory - Results and graphics will be output to this directory. Files will be overwritten.
5. reference_loci1.fasta - Fasta DNA or amino-acid sequence input. Multiple loci should be provided as separate files. Each genome in the fasta files should have a subtype assignment in the subtype_assignment_file.

Options:

1. --aa - Set flag when input is amino-acid sequences. Default is nucleotide.
2. --config /path/to/file - Phylotyper config file. Can also be set in environment variable PHYLOTYPER_CONFIG. See Setting up Phylotyper config file.
3. --index /path/to/file - YAML-format file that lists the locations of subtype reference files. You can specify a file that is not the default file packaged with phylotyper.
4. --description - A help description for the subtype scheme.

If you would like to contribute a subtype scheme to the main repository, please contact me, Matt Whiteside [email protected].

Input Formats for New Pipeline:

Input sequence files are required to be in fasta format. If the subtype scheme involves multiple gene/loci, there should be one file per gene with all copies of the gene in the same file. The order of the gene files determines their order in the superalignment. A genome can have multiple copies of a gene/loci. To indicate a genome with multiple copies/alleles of the same gene, format the fasta header as follows:

>lcl|genome_identifier|allele_identifier

or

>genome_identifier|allele_identifier

The subtype file is a tab-delimited text file containing two colums:

genome_identifier<\tab>subtype

CONTRIBUTING TO PHYLOTYPER

We would welcome any updates, new user subtype schemes or suggestions for new subtype schemes. We will add submitted subtype schemes to the Phylotyper repository. Please contact me at [email protected].

ABOUT PHYLOTYPER

Ancestral State Reconstruction

Phylotyper employs a Hidden State Prediction (HSP) algorithm to predict subtypes for unannotated strains. HSP itself is an extension of Ancestral State Reconstruction (ASR). These algorithms use phylogenetic models to predict features or properties. ASR estimates properties of ancestral organisms from the properties of the extant descendents in the tree. In contrast, HSP estimates the properties of a limited number of unannotated strains at the tips of the tree. Both methods use an inferred phylogenetic tree built from a reference set of sequences with known subtype. The algorithms calculate subtype states, for ancestors in ASR, or for unannotated tips and ancestors in HSP, that maximizes the likelihood given the observed subtype states in the tips and the estimated model of subtype evolution and phylogeny. In Phylotyper we use the rerootingMethod function from the Phytools R package. This function can estimate discrete properties such as subtypes for unknown tip nodes. Internally, rerootingMethod uses the ASR method of Yang et al., 2006 which estimates the marginal likelihood of all subtype states at the root of the tree. To estimate tip states for HSP, the Phytools function roots the tree at the unannotated tip and runs the Yang algorithm to calculate, in this case, the empirical baysian estimate of the tip's state.

For more information, see Zaneveld, J & Thurber R, 2014 for a general review of HSP and its applications, and the Phytools manual for details on the rerootingMethod used in Phylotyper.

Steps in the Phylotyper pipeline

1. Identify subtype gene loci in input genomes using blastn or blastx depending on subtype sequence type. For each gene loci found in the input genomes:
2. Compare input gene against reference genes. If an identical reference gene found, report subtype and terminate at this point. If no identical sequences found, proceed with Phylotyper analysis.
3. Align input genes against a pre-aligned set of reference genes using the tool MAFFT's --add option.
4. Automatically trim alignment using tool trimAI.
5. If multiple loci are involved, concatenate individual alignments into superalignment.
6. Generate maximum likelihood phylogenetic tree of aligned genes with FastTree.
7. Run phytools rerootingMethod using the phylogenetic tree and assigned subtypes.
8. Identify the subtype with maximum marginal likelihood for the unknown gene.

Adding new subtype schemes

Phylotyper includes functionality to allow you to add your own subtype schemes. Schemes can be one or more loci (currently no limit defined, however, we have only tested with two loci). The sequences can be nucleotide or amino acid. The new subtype pipeline automatically generates and stores all required input files, so that future subtype prediction runs only have to reference a subtype name.

Reference files

Phylotyper reference files and their locations for available subtype schemes are defined in a YAML-format file. The default subtype file is <package_name>/phylotyper/subtype_index.yaml. This file can be specified using the --index option. The subtype_index.yaml file is automatically updated when new subtypes are created. In subtype_index.yaml, the root field specifies the parent data directory. If a relative path is provided, the data directory is a subdirectory of <package_name>/phylotyper/. The default is <package_name>/phylotyper/data. Each subtype scheme will have a subdirectory under this root data directory. The subtypes field in subtype_index.yaml is a list of all subtypes indexed by name. Under a subtype the following files/options will be defined:

1. alignment: the reference sequence alignment
2. desc: Verbal description of subtype scheme defined in new arguments
3. lookup: JSON object containing all reference sequences
4. nloci: Number of loci in scheme
5. rate_matrix: emperical transition matric for the Mk model
6. search_database: BLAST database for searching genomes
7. seq: sequence type (nt|aa)
8. subtype: tab-delimited file listing genomes (column 1) and subtypes (column 2)

Multiple loci

Multiple loci can be used in a Phylotyper subtype scheme. For example, schemes stx1, stx2, wz all use two genes. The individual loci will be BLAST'd and aligned independently. The individual loci alignments are concatenated to form a superalignment. The superalignment is used as input into the phylogenetic tree building step.

Parameterization of the transition matrix

Phylotyper offers flexibility in the parameterization of evolution model used in the ASR step. A component of the underlying ASR framework, is an Mk or markov model of subtype evolution, for which an emperical transition rate matrix is estimated from the data. The transition matrix is used to calculate the expected number of subtype state changes given a distance in the phylogenetic tree. Different model parameterizations can be defined for the transition rate matrix. The simplest parameterization available in Phylotyper is the equal rates model; all subtypes have the same forward and reverse rate. The most complex parameterization available in Phylotyper is the symmetric model, wherein each forward and reverse rate for a given pair of subtypes are assigned a separate parameter. Frequently, the number of subtypes makes the symmetric model too computationally prohibitive (it is unavailable for schemes with >10 subtypes). To offer more flexible models in these situations with reduced numbers of free parameters, two custom parameterization approaches were developed. The custom approaches both use a binning strategy that attempts to identify sets of subtypes that would have similar rates and assign them a single parameter as a set.

1. Small-distance binning: The rationale is to select the closest subtypes in the phylogenetic tree as free parameters. Subtypes with large distances are assigned a common parameter. Maximum inter-patristic distances are collected for all subtypes and modelled as a normal mixture distribution. The smallest normal distribution is selected (based on mean) and all pairs of subtypes belonging to this distribution are set as a free parameters. Other subtypes are assigned a common parameter.

2. Iterateive binning: The rationale is to approximate the transition rates individually for each subtype pair, cluster subtypes by the approximate rates and then assign each cluster a separate parameter. Each subtype pair (forward and reverse directions) are set as a free parameter while fixing all other parameters. The Mk model estimation is run and transition rate is recorded. The collected transition rates are clustered using Mclust. Each cluster is assigned a separate parameter.

Each of these model parameterizations; equal, symmetric and the two custom models are tested and evaluated in new subtype pipeline. The parameterization that has highest accuracy (based on a leave-one-out cross-validation analysis) is selected. In the case of ties, the model with the fewest parameters is given precidence (the symmetric model is not tested when the number of subtypes is over 10)

Evaluating new subtype schemes

Phylotyper conducts two tests for subtypes schemes submitted to the new pipeline.

Check 1. Clades with relatively small inter-patristic distance have the same subtype

The purpose of the first check is to identify isolated cases of distinct subtypes that are clustered together in the phylogenetic tree. In large-scale cases, descendent clades in the phylogenetic tree with multiple distinct subtypes may indicate a subtype that is not correlated with the phylogeny. In limited cases, it might indicate annotation errors. Phylotyper computes an inter-patritristic distances for all leaves in the subtype phylogenetic tree for the given subtype scheme. It then computes a threshold is equivalent to 0.4 probability that inter-patristic distances equal to or greater then threshold belong to the same-subtype distribution. To estimate the distributions, all inter-patristic distances for nodes with the same subtype and all distances for nodes with different subtypes are fit with R's Mclust package. Subtrees with a max inter-patristic distance less than this threshold that have distinct subtypes are flagged. You will be notified if this situation is detected. An updated subtype input file called phylotyper_proposed_subtypes.csv will be generated with proposed corrections and written to the output directory.

Check 2. The predictive performance is above a minimum threshold

All new subtype schemes are subject to a leave-one-out cross-validation analysis that assesses the performance of the given phylogeny to predict the subtype. In the leave-out-out cross-validation simulation, the subtype label of each gene in the training set is removed, one at a time, and the remaining genes in training set are used to predict the subtype of the test gene. Positive and negative results are required and the F1-score, which is a weighted average of the precision and recall, is calculated. Precision is defined as:

Precision = TP / (TP + FP)

and recall as:

Recall = TP / (TP + FN)

These values are then combined to produce an F-score as follows:

2 * ( precision * recall ) / ( precision + recall )

TP = TruePositive, FP = False Positive, FN = False Negative

The F-score; a binary classifer metric, was recorded individually for each subtype and then averaged to create a single performance metric for this multi-class predictor. You will be notified if the F1-score (a equally weighted average of precision and recall) is below 0.9.

CONTACT

Matt Whiteside [email protected] Vic Gannon [email protected]

TODO