eMPRess: a systematic cophylogeny reconciliation tool

2020 ◽  
Author(s):  
Santi Santichaivekin ◽  
Qing Yang ◽  
Jingyi Liu ◽  
Ross Mawhorter ◽  
Justin Jiang ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Tree Reconciliation ◽  
Loss Model ◽  
Software Program

Abstract Summary We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences. Availability and implementation eMPRess is freely available at http://www.cs.hmc.edu/empress. Supplementary information Supplementary data are available at Bioinformatics online.

DoubleRecViz: a web-based tool for visualizing transcript–gene–species tree reconciliation

2020 ◽  
Author(s):  
Esaie Kuitche ◽  
Yanchun Qi ◽  
Nadia Tahiri ◽  
Jack Parmer ◽  
Aïda Ouangraoua
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Source Code ◽  
Species Tree ◽  
Supplementary Information ◽  
Dynamic Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Tree Reconciliation ◽  
Transcript Gene

Abstract Motivation A phylogenetic tree reconciliation is a mapping of one phylogenetic tree onto another which represents the co-evolution of two sets of taxa (e.g. parasite–host co-evolution, gene–species co-evolution). The reconciliation framework was extended to allow modeling the co-evolution of three sets of taxa such as transcript–gene–species co-evolutions. Several web-based tools have been developed for the display and manipulation of phylogenetic trees and co-phylogenetic trees involving two trees, but there currently exists no tool for visualizing the joint reconciliation between three phylogenetic trees. Results Here, we present DoubleRecViz, a web-based tool for visualizing double reconciliations between phylogenetic trees at three levels: transcript, gene and species. DoubleRecViz extends the RecPhyloXML model—developed for gene–species tree reconciliation—to represent joint transcript–gene and gene–species tree reconciliations. It is implemented using the Dash library, which is a toolbox that provides dynamic visualization functionalities for web data visualization in Python. Availability and implementation DoubleRecViz is available through a web server at https://doublerecviz.cobius.usherbrooke.ca. The source code and information about installation procedures are also available at https://github.com/UdeS-CoBIUS/DoubleRecViz. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Capybara: equivalence ClAss enumeration of coPhylogenY event-BAsed ReconciliAtions

2020 ◽  
Vol 36 (14) ◽  
pp. 4197-4199
Author(s):  
Yishu Wang ◽  
Arnaud Mary ◽  
Marie-France Sagot ◽  
Blerina Sinaimeri
Keyword(s):  
Source Code ◽  
Supplementary Information ◽  
Optimal Solutions ◽  
Supplementary Data ◽  
Huge Number ◽  
Tree Reconciliation ◽  
Class Enumeration ◽  
Suboptimal Solutions ◽  
The Many ◽  
Event Based

Abstract Motivation Phylogenetic tree reconciliation is the method of choice in analyzing host-symbiont systems. Despite the many reconciliation tools that have been proposed in the literature, two main issues remain unresolved: (i) listing suboptimal solutions (i.e. whose score is ‘close’ to the optimal ones) and (ii) listing only solutions that are biologically different ‘enough’. The first issue arises because the optimal solutions are not always the ones biologically most significant; providing many suboptimal solutions as alternatives for the optimal ones is thus very useful. The second one is related to the difficulty to analyze an often huge number of optimal solutions. In this article, we propose Capybara that addresses both of these problems in an efficient way. Furthermore, it includes a tool for visualizing the solutions that significantly helps the user in the process of analyzing the results. Availability and implementation The source code, documentation and binaries for all platforms are freely available at https://capybara-doc.readthedocs.io/. Contact [email protected] or [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

HaploGrouper: a generalized approach to haplogroup classification

2020 ◽  
Author(s):  
Anuradha Jagadeesan ◽  
S Sunna Ebenesersdóttir ◽  
Valdis B Guðmundsdóttir ◽  
Elisabet Linda Thordardottir ◽  
Kristjan H S Moore ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Tree ◽  
Y Chromosome ◽  
State Of The Art ◽  
Supplementary Information ◽  
Sequence Variants ◽  
Use Case ◽  
Supplementary Data ◽  
Human Mitochondrial Dna ◽  
Comparable Accuracy

Abstract Motivation We introduce HaploGrouper, a versatile software to classify haplotypes into haplogroups on the basis of a known phylogenetic tree. A typical use case for this software is the assignment of haplogroups to human mitochondrial DNA (mtDNA) or Y-chromosome haplotypes. Existing state-of-the-art haplogroup-calling software is typically hard-wired to work only with either mtDNA or Y-chromosome haplotypes from humans. Results HaploGrouper exhibits comparable accuracy in these instances and has the advantage of being able to assign haplogroups to any kind of haplotypes from any species—given an extant annotated phylogenetic tree defined by sequence variants. Availability and implementation The software is available at the following URL https://gitlab.com/bio_anth_decode/haploGrouper. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation

2020 ◽  
Author(s):  
Chayan Kumar Saha ◽  
Rodrigo Sanches Pires ◽  
Harald Brolin ◽  
Maxence Delannoy ◽  
Gemma Catherine Atkinson
Keyword(s):  
Phylogenetic Tree ◽  
Supplementary Information ◽  
Evolutionary Analysis ◽  
Gene Conservation ◽  
Supplementary Data ◽  
Web Tool ◽  
Cluster Evolution ◽  
Graphical Visualization ◽  
Molecular Evolutionary Analysis ◽  
The Web

Abstract Summary Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin–antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run. Availability and implementation FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals ccNetViz: a WebGL-based JavaScript library for visualization of large networks

2020 ◽  
Vol 36 (16) ◽  
pp. 4527-4529
Author(s):  
Ales Saska ◽  
David Tichy ◽  
Robert Moore ◽  
Achilles Rasquinha ◽  
Caner Akdas ◽  
...  
Keyword(s):  
Systems Biology ◽  
Complex Networks ◽  
Open Source ◽  
High Speed ◽  
A Priori ◽  
Supplementary Information ◽  
Network Visualization ◽  
Supplementary Data ◽  
Web Based ◽  
Flow Of Information

Abstract Summary Visualizing a network provides a concise and practical understanding of the information it represents. Open-source web-based libraries help accelerate the creation of biologically based networks and their use. ccNetViz is an open-source, high speed and lightweight JavaScript library for visualization of large and complex networks. It implements customization and analytical features for easy network interpretation. These features include edge and node animations, which illustrate the flow of information through a network as well as node statistics. Properties can be defined a priori or dynamically imported from models and simulations. ccNetViz is thus a network visualization library particularly suited for systems biology. Availability and implementation The ccNetViz library, demos and documentation are freely available at http://helikarlab.github.io/ccNetViz/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Epidemiological modeling in StochSS Live!

2021 ◽  
Author(s):  
Richard Jiang ◽  
Bruno Jacob ◽  
Matthew Geiger ◽  
Sean Matthew ◽  
Bryan Rumsey ◽  
...  
Keyword(s):  
Stochastic Model ◽  
Epidemiological Model ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Web Based ◽  
Epidemiological Modeling ◽  
Modeling Simulation ◽  
Wide Range ◽  
Biochemical Systems

Abstract Summary We present StochSS Live!, a web-based service for modeling, simulation and analysis of a wide range of mathematical, biological and biochemical systems. Using an epidemiological model of COVID-19, we demonstrate the power of StochSS Live! to enable researchers to quickly develop a deterministic or a discrete stochastic model, infer its parameters and analyze the results. Availability and implementation StochSS Live! is freely available at https://live.stochss.org/ Supplementary information Supplementary data are available at Bioinformatics online.

KEC: unique sequence search by K-mer exclusion

2021 ◽  
Author(s):  
Pavel Beran ◽  
Dagmar Stehlíková ◽  
Stephen P Cohen ◽  
Vladislav Čurn
Keyword(s):  
Amino Acid ◽  
Nucleic Acid ◽  
Source Code ◽  
Unique Sequence ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Laptop Computers ◽  
Sequence Search ◽  
Target Sequences ◽  
Cross Reference

Abstract Summary Searching for amino acid or nucleic acid sequences unique to one organism may be challenging depending on size of the available datasets. K-mer elimination by cross-reference (KEC) allows users to quickly and easily find unique sequences by providing target and non-target sequences. Due to its speed, it can be used for datasets of genomic size and can be run on desktop or laptop computers with modest specifications. Availability and implementation KEC is freely available for non-commercial purposes. Source code and executable binary files compiled for Linux, Mac and Windows can be downloaded from https://github.com/berybox/KEC. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CorGAT: a tool for the functional annotation of SARS-CoV-2 genomes

2020 ◽  
Author(s):  
Matteo Chiara ◽  
Federico Zambelli ◽  
Marco Antonio Tangaro ◽  
Pietro Mandreoli ◽  
David S Horner ◽  
...  
Keyword(s):  
Functional Annotation ◽  
Ad Hoc ◽  
State Of The Art ◽  
Supplementary Information ◽  
Genomic Sequences ◽  
Supplementary Data ◽  
Evolutionary Patterns ◽  
Genomic Variants ◽  
Art Methods ◽  
Available Resources

Abstract Summary While over 200 000 genomic sequences are currently available through dedicated repositories, ad hoc methods for the functional annotation of SARS-CoV-2 genomes do not harness all currently available resources for the annotation of functionally relevant genomic sites. Here, we present CorGAT, a novel tool for the functional annotation of SARS-CoV-2 genomic variants. By comparisons with other state of the art methods we demonstrate that, by providing a more comprehensive and rich annotation, our method can facilitate the identification of evolutionary patterns in the genome of SARS-CoV-2. Availabilityand implementation Galaxy   http://corgat.cloud.ba.infn.it/galaxy; software: https://github.com/matteo14c/CorGAT/tree/Revision_V1; docker: https://hub.docker.com/r/laniakeacloud/galaxy_corgat. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals UniBioDicts: Unified access to Biological Dictionaries

2020 ◽  
Author(s):  
John Zobolas ◽  
Vasundra Touré ◽  
Martin Kuiper ◽  
Steven Vercruysse
Keyword(s):  
User Interface ◽  
Life Science ◽  
Biological Data ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Query Interface ◽  
Controlled Vocabularies ◽  
Search String ◽  
Software Packages ◽  
The Right

Abstract Summary We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms. Availability and implementation The UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals CONCUR: quick and robust calculation of codon usage from ribosome profiling data

2020 ◽  
Author(s):  
Michaela Frye ◽  
Susanne Bornelöv
Keyword(s):  
Codon Usage ◽  
Ribosome Profiling ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Usage Analysis

Abstract Summary CONCUR is a standalone tool for codon usage analysis in ribosome profiling experiments. CONCUR uses the aligned reads in BAM format to estimate codon counts at the ribosome E-, P- and A-sites and at flanking positions. Availability and implementation CONCUR is written in Perl and is freely available at https://github.com/susbo/concur. Supplementary information Supplementary data are available at Bioinformatics online.

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