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Multiple nucleotide sequence alignment evaluation software tools | Comparative genomics

Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence analyses from molecular phylogenetics to 3D structure prediction. Sophisticated algorithms have been developed for sequence alignment, but in practice, many…
PSAR-align
Desktop

PSAR-align

A multiple sequence realignment tool that can refine a given multiple sequence…

A multiple sequence realignment tool that can refine a given multiple sequence alignment based on suboptimal alignments generated by probabilistic sampling. PSAR-Align is able to improve the results…

TCS
Desktop
Web

TCS Transitive Consistency Score

An alignment evaluation score that makes it possible to identify in an MSA the…

An alignment evaluation score that makes it possible to identify in an MSA the most correct positions. It has been shown that these positions are the most likely to be structurally correct and also…

GUIDANCE
Web

GUIDANCE

An integrative methodology that accounts for: (i) uncertainty in the process of…

An integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments,…

AcCNET
Desktop

AcCNET Accessory Genome Constellation Network

Aims to compare accessory genomes of a large number of genomic units, both at…

Aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. The AcCNET workflow comprises three steps: (i) protein cluster construction, (ii)…

GMA
Desktop

GMA Genome Mappability Analyzer

Computes the GMS of every position in a genome. The GMA leverages the…

Computes the GMS of every position in a genome. The GMA leverages the parallelism of cloud computing to analyze large genomes, and enabled us to identify the 5–14% of the human, mouse, fly and yeast…

OD-seq
Desktop

OD-seq

A practical and simple method to detect outliers in multiple sequence…

A practical and simple method to detect outliers in multiple sequence alignments (MSAs). OD-seq can also detect outliers in sets of unaligned sequences, but with reduced accuracy. For medium sized…

FastSP
Desktop

FastSP

Calculates the Developer score, Modeler score, Total Column score and Cline…

Calculates the Developer score, Modeler score, Total Column score and Cline Shift Score. FastSP is a basic tool for analyzing sets of multiple sequence alignments. It can be used to evaluate the…

trimAl
Desktop
Web

trimAl

A tool for automated alignment trimming, which is especially suited for…

A tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the…

ZORRO
Desktop

ZORRO

A probabilistic masking program that objectively measures the quality of the…

A probabilistic masking program that objectively measures the quality of the alignment at each individual position. ZORRO uses a pair Hidden Markov Model (pair-HMM) to model the sequence evolution…

Aliscore
Desktop

Aliscore

Identifies random similarity within multiple sequence alignments based on Monte…

Identifies random similarity within multiple sequence alignments based on Monte Carlo resampling within a sliding window. Aliscore infers similarity profiles from pairwise sequence comparisons and…

MaxAlign
Web
Desktop

MaxAlign

Removes sequences (taxa) with many gaps in the post-process of alignments in…

Removes sequences (taxa) with many gaps in the post-process of alignments in order to improve the alignment area. MaxAlign optimizes the alignment prior to such analyses. It maximizes the number of…

MergeAlign
Web

MergeAlign

Constructs a consensus multiple sequence alignment from multiple independent…

Constructs a consensus multiple sequence alignment from multiple independent alignments. Using dynamic programming MergeAlign efficiently combines individual multiple sequence alignments to generate…

ezBAMQC
Desktop

ezBAMQC

Allows user to verify the quality of one or more next generation mapped…

Allows user to verify the quality of one or more next generation mapped datasets. ezBAMQC conducts comprehensive assessments of harmonized sequencing data from multiple perspectives, including:…

PanCanQC
Desktop

PanCanQC

Allows to calculate and estimate the quality control (QC) values which are used…

Allows to calculate and estimate the quality control (QC) values which are used in the International Cancer Genome Consortium (ICGC) PanCan project.

Noisy
Desktop

Noisy

A method that, based on assessing the distribution of character states along a…

A method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple…

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