AF | Dataset: unassembled-plants

Dataset description

The dataset pertains to unassembled reads from 14 plant species. This data set was originally compiled by Hatje and Kollmar (2012) This set of genomes was prepared separately for 7 different sequencing coverages: 0.015625, 0.03125, 0.0625, 0.125, 0.25, 0.5, 1.0. ART software was used to simulate unassembled reads from complete genome sequences.

Dataset file structure

The dataset has 7 directories, each directory has 14 files, 98 files in total.

unassembled-plants
├── coverage_0.015625
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   ├── clementin.fasta
│   ├── grandis.fasta
│   ├── halophilu.fasta
│   ├── lyrata.fasta
│   ├── papaya.fasta
│   ├── parvulum.fasta
│   ├── raimondii.fasta
│   ├── rapa.fasta
│   ├── rubella.fasta
│   ├── sinensis.fasta
│   ├── thalian.fasta
│   └── vinifera.fasta
├── coverage_0.03125
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   └── ...
├── coverage_0.0625
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   └── ...
├── coverage_0.125
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   └── ...
├── coverage_0.25
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   └── ...
├── coverage_0.5
│   ├── cacao.fasta
│   ├── camaldule.fasta
│   └── ...
└── coverage_1
    ├── cacao.fasta
    ├── camaldule.fasta
    └── ...

Benchmark Protocol

The test evaluates an accuracy of alignment-free distance measures in reconstructing species phylogeny based on unassembled genome sequences and varying set of sequencing coverages.

Specifically, the benchmark procedure takes as input 7 user's files with, either all-versus all distances or phylogenetic tree in Newick format. For each file, the distances are used as input into the neighbour-joining algorithm (fneighbor from EMBOSS:6.3.1 PHYLIPNEW:3.69) to generate the corresponding method tree. To assess the accuracy of method tree we computed the Robinson-Foulds distance between a tree computed using that method (the “test tree”) and the corresponding species tree, using ftreedist (EMBOSS:6.3.1 PHYLIPNEW:3.69). The overall assesment of method accuracy is an average of RF distance values across 7 trees.

Testing your own method

Download from the server the dataset file: unassembled-plants.zip. Unzip the downloaded file.

Use the unzipped 7 FASTA files as an input to your method and calculate either, the distances between every pair of sequences or phylogenetic tree (see File Formats below).

Save the results to 7 text files.

Submit you predictions (upload 7 output files) to the web server.

The web service benchmarks the uploaded results and presents a report with the submitted method's performance and comparison to other available methods. Additionally, you can choose to make the report publicly available.

Download dataset

File name: unassembled-plants.zip

File size: 2.7 GB

MD5sum: 90ae0609e1c124e15461e49197c8d4c6

File formats supported in benchmark

Benchmark supports one of the following file formats:

Tap-Separated Value Format (TSV)

Simple simple text file with three tab-separated columns: first two columns store identifiers of two sequences being compared, and third column has a numerical distance value of this comparison.

Example of Text File Format (4 sequences)

A   B   8.876
A   C   6.120
A   D   4.321
B   C   5.231
B   D   3.983
C   D   0.663

Phylip Distance Matrix

Square Distance matix in Phylip format

Example of Phylip distance matrix (for 4 sequences)

   4
A        0.000 8.876 6.120 9.321
B        8.876 0.000 2.231 3.983
C        6.120 2.231 0.000 0.663
D        9.321 3.983 0.663 0.000

Lower-triangle Distance matix in Phylip format

Example of Phylip distance matrix (for 4 sequences)

   4
A
B        8.876
C        6.120 2.231
D        9.321 3.983 0.663

Newick Tree

Tree in Newick format

Example of Newick Format (4 sequences)

(B,(C,D),A);

Branch lengths can be incorporated, but are not required.

(B:2.13125,(C:0.90675,D:1.56975):0.64425,A:6.74475);

Genome-based Phylogeny

Plants (plants)