The reference dataset pertains to protein sequences collected from SwissTree release 2017.9. SwissTree is a collection of large- and high-confidence gene family phylogenies with different types of challenges for sequence comparison and species from all domains.
The FASTA file is a mixture of 11 SwissTree gene families.
| # | Gene Family short name | Gene Family name | Number of sequences |
|---|---|---|---|
| 1 | ST001 | Popeye domain-containing protein family | 49 |
| 2 | ST002 | NOX 'ancestral-type' subfamily NADPH oxidases | 54 |
| 3 | ST003 | V-type ATPase beta subunit | 49 |
| 4 | ST004 | Serine incorporator family | 115 |
| 5 | ST005 | SUMF family | 29 |
| 6 | ST007 | Ribosomal protein S10/S20 | 60 |
| 7 | ST008 | Bambi family | 42 |
| 8 | ST009 | Asterix family | 39 |
| 9 | ST010 | Cited family | 34 |
| 10 | ST011 | Glycosyl hydrolase 14 family | 159 |
| 11 | ST012 | Ant transformer protein | 21 |
The dataset has 1 directory containing 651 FASTA files
swisstree ├── ST001_001.fasta ├── ST001_002.fasta ├── ST001_003.fasta ├── ST001_004.fasta ├── ST001_005.fasta ├── ST001_006.fasta ├── ST001_007.fasta ├── ST001_008.fasta ├── ST001_009.fasta ├── ST001_010.fasta ├── ...
The test evaluates an accuracy of alignment-free distance measures in phylogenetic reconstruction of gene families.
Specifically, the benchmark procedure takes as input user's file containing the distances between all sequence pairs present in the dataset file. Only distances between protein pairs from the same family are extracted.
For each family, 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 reference tree in SwissTree, using ftreedist (EMBOSS:6.3.1 PHYLIPNEW:3.69).
To facilitate comparison of results sequence sets (hence trees) of different sizes N, we normalize this distance according to the maximum possible distance between two unrooted trees, 2(N − 3). We denote this normalised Robinson-Foulds distance as nRF, with a value from 0 to 1 that can be interpreted as the proportion of false or missing bipartitions in the test-tree topology compared to the reference topology. When RF = 0 the test and reference topologies are identical, implying high accuracy for the method. Conversely, at RF = 1 no bipartition in the reference is recovered. The overall assesment of method accuracy is weighted average of nRFs across all 11 gene families.
File name: swisstree.zip
File size: 298.2 KB
MD5sum: 813d5f7f9c50fdd57001592c9da9e5f1
Benchmark supports one of the following file formats:
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
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