A greedy alignment-free distance estimator for phylogenetic inference

Thankachan, Sharma V.; Chockalingam, Sriram P.; Liu, Yongchao; Krishnan, Ambujam; Aluru, Srinivas

doi:10.1186/s12859-017-1658-0

Cited by 28 publications

(31 citation statements)

References 29 publications

(30 reference statements)

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“…For such data, standard two-phase methods that first compute an alignment and then compute a tree do not have acceptable accuracy, while PASTA [32], BAli-Phy [33], and other co-estimation methods are not fast. It is possible that alignment-free methods (see [34,35,36] for an entry into this topic) might provide good starting trees, but these have not been tested on ultra-large datasets (with thousands of species), and have instead mainly been focused on genome-scale analyses of tens of genomes. However, for any large dataset on which the starting trees cannot be reasonably accurately estimated quickly, blended DTM divide-and-conquer strategies may provide the best accuracy.…”

Section: Discussionmentioning

confidence: 99%

Unblended Disjoint Tree Merging using GTM improves species tree estimation

Smirnov

Warnow

2019

Preprint

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AbstractPhylogeny estimation is an important part of much biological research, but large-scale tree estimation is infeasible using standard methods due to computational issues. Recently, an approach to large-scale phylogeny has been proposed that divides a set of species into disjoint subsets, computes trees on the subsets, and then merges the trees together using a computed matrix of pairwise distances between the species. The novel component of these approaches is the last step: Disjoint Tree Merger (DTM) methods. We present GTM (Guide Tree Merger), a polynomial time DTM method that adds edges to connect the subset trees, so as to provably minimize the topological distance to a computed guide tree. Thus, GTM performs unblended mergers, unlike the previous DTM methods. Yet, despite the potential limitation, our study shows that GTM has excellent accuracy, generally matching or improving on two previous DTMs, and is much faster than both. Thus, the GTM approach to the DTM problem is a useful new tool for large-scale phylogenomic analysis, and shows the surprising potential for unblended DTM methods. The software for GTM is available at https://github.com/vlasmirnov/GTM.

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Section: Discussionmentioning

confidence: 99%

Unblended Disjoint Tree Merging using GTM improves species tree estimation

Smirnov

Warnow

2019

Preprint

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“…In this study, the results based on 14 dissimilarity measures are evaluated. ALFRED-G [57] uses an efficient algorithm to calculate the length of maximal k-mismatch common substrings between two sequences. Specifically, to measure the degree of dissimilarity between two nucleic acid or protein sequences, the program calculates the length of maximal word pairs -one word from each of the sequences -with up to k mismatches.…”

Section: Alignment-free Toolsmentioning

confidence: 99%

Benchmarking of alignment-free sequence comparison methods

Zieleziński

Girgis

Bernard

et al. 2019

Preprint

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2 Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures have been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment. Here, we present a community resource (http://afproject.org) to establish standards for comparing alignment-free approaches across different areas of sequence-based research. We characterize 74 AF methods available in 24 software tools for five research applications, namely, protein sequence classification, gene tree inference, regulatory element detection, genome-based phylogenetic inference and reconstruction of species trees under horizontal gene transfer and recombination events.The interactive web service allows researchers to explore the performance of alignmentfree tools relevant to their data types and analytical goals. It also allows method developers to assess their own algorithms and compare them with current state-of-theart tools, accelerating the development of new, more accurate AF solutions. BACKGROUNDComparative analysis of DNA and amino acid sequences is of fundamental importance in biological research, particularly in molecular biology and genomics. It is the first and key step in molecular evolutionary analysis, gene function and regulatory region prediction, sequence assembly, homology searching, molecular structure prediction, gene discovery and protein structure-function relationships analysis. Traditionally, sequence comparison was based on pairwise or multiple sequence alignment (MSA). Software tools for sequence alignment, such as BLAST [1] and CLUSTAL [2], are the most widely used bioinformatics methods.Although alignment-based approaches generally remain the references for sequence

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“…These approaches are also very efficient, since common substrings can be rapidly found using suffix trees or related data structures [55,27]. As a generalization of this approach, some methods use longest common substrings with a certain number of mismatches [30,54,53,33,3].…”

Section: Introductionmentioning

confidence: 99%

Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees

Dencker

Leimeister

Gerth

et al. 2018

Lecture Notes in Computer Science

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Motivation: Word-based or 'alignment-free' methods for phylogeny reconstruction are much faster than traditional approaches, but they are generally less accurate. Most of these methods calculate pairwise distances for a set of input sequences, for example from word frequencies, from so-called spaced-word matches or from the average length of common substrings. Results: In this paper, we propose the first word-based approach to tree reconstruction that is based on multiple sequence comparison and Maximum Likelihood. Our algorithm first samples small, gap-free alignments involving four taxa each. For each of these alignments, it 1 arXiv:1803.09222v2 [q-bio.PE] 28 Apr 2018 then calculates a quartet tree and, finally, the program Quartet Max-Cut is used to infer a super tree topology for the full set of input taxa from the calculated quartet trees. Experimental results show that trees calculated with our approach are of high quality. Availability: The source code of the program is available at https://github.com/tdencker/multi-SpaM

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A greedy alignment-free distance estimator for phylogenetic inference

Cited by 28 publications

References 29 publications

Unblended Disjoint Tree Merging using GTM improves species tree estimation

Unblended Disjoint Tree Merging using GTM improves species tree estimation

Benchmarking of alignment-free sequence comparison methods

Multi-SpaM: A Maximum-Likelihood Approach to Phylogeny Reconstruction Using Multiple Spaced-Word Matches and Quartet Trees

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