SoRT2: a tool for sorting genomes and reconstructing phylogenetic trees by reversals, generalized transpositions and translocations

Abstract

SoRT(2) is a web server that allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. It takes as input two or more linear/circular multi-chromosomal gene (or synteny block) orders in FASTA-like format. When the input is two genomes, SoRT(2) will quickly calculate their rearrangement distance, as well as a corresponding optimal scenario by highlighting the genes involved in each rearrangement operation. In the case of multiple genomes, SoRT(2) will also construct phylogenetic trees of these genomes based on a matrix of their pairwise rearrangement distances using distance-based approaches, such as neighbor-joining (NJ), unweighted pair group method with arithmetic mean (UPGMA) and Fitch-Margoliash (FM) methods. In addition, if the function of computing jackknife support values is selected, SoRT(2) will further perform the jackknife analysis to evaluate statistical reliability of the constructed NJ, UPGMA and FM trees. SoRT(2) is available online at http://bioalgorithm.life.nctu.edu.tw/SORT2/.

Figure 1.

(a) User interface of SoRT². (b) Display of an optimal rearrangement scenario in which the genes involved in rearrangements are highlighted. (c) A pairwise rearrangement distance matrix obtained when applying SoRT² to six mammalian genomes with 1360 synteny blocks. (d) A phylogenetic tree of six mammalian genomes produced by SoRT² with jackknife support values on its clades.

Figure 2.

Accuracy comparison of SoRT² and GRIMM-NJ for their phylogenetic tree reconstruction based on three different ratios of reversals, transpositions and translocations: (a) 1:0:1, (b) 2:1:2 and (c) 1:1:1, where vertical axis indicates average tree similarity (%) and horizontal axis indicates species number.

Figure 3.

(a) The reference tree of 11 metazoan gene orders adopted from ref. (1), where the 11 metazoan organisms are grouped into six major groupings: Chordate (with HU), Echinoderm (with SS and SU), Arthropod (with DR and AF), Mollusk (with KT, AC and CN), Annelid (with LU) and Nematode (with OV and AS). (b) The NJ tree produced by SoRT² using a jackknife analysis of 100 replicates, where numbers on internal nodes denote the support values. (c) The NJ tree based on the pairwise rearrangement distances calculated by GRIMM. (d) The phylogenetic tree reconstructed by MGR.

Figure 4.

(a) The reference tree of six mammalian genomes adopted from ref. (29), where its edges were not drawn to scale. (b) The NJ tree created by SoRT² using a jackknife analysis of 100 replicates, where numbers on internal nodes are the support values. (c) The NJ tree based on the pairwise rearrangement distances returned by GRIMM.

Figure 5.

(a) The NJ tree constructed by SoRT² using a jackknife analysis of 100 replicates, where numbers on internal nodes are the support values. (b) The NJ tree based on the pairwise rearrangement distances computed by GRIMM. (c) The phylogenetic tree created by MGR.