Reference health
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
44/44 checkable references clean · checked 2026-07-21
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
1 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 44 checked references that resolve
resolves10.1002/(SICI)1097-0134(19980701)32:1<88::AID-PROT10>3.0.CO;2-J
Generalized affine gap costs for protein sequence alignment
resolves10.1016/0022-2836(87)90316-0
A strategy for the rapid multiple alignment of protein sequences
resolves10.1093/bioinformatics/7.4.479
A novel randomized iterative strategy for aligning multiple protein sequences
resolves10.1186/1471-2105-3-2
The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
resolves10.1093/nar/gkn879
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
resolves10.1186/gb-2010-11-4-r37
Phylogenetic assessment of alignments reveals neglected tree signal in gaps
resolves10.1007/BF02603120
Progressive sequence alignment as a prerequisitetto correct phylogenetic trees
resolves10.1093/molbev/msm176
Mind the Gaps: Evidence of Bias in Estimates of Multiple Sequence Alignments
resolves10.1093/bioinformatics/9.3.361
Optimal alignment between groups of sequences and its application to multiple sequence alignment
resolves10.1093/bioinformatics/11.5.543
A weighting system and aigorithm for aligning many phylogenetically related sequences
resolves10.1016/0378-1119(88)90330-7
CLUSTAL: a package for performing multiple sequence alignment on a microcomputer
resolves10.1093/bioinformatics/8.3.275
The rapid generation of mutation data matrices from protein sequences
resolves10.1093/bioinformatics/bts578
Adding unaligned sequences into an existing alignment using MAFFT and LAST
resolves10.1093/nar/gkf436
MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
resolves10.1093/bioinformatics/btl592
PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences
resolves10.1186/1471-2105-9-212
Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework
resolves10.1093/bioinformatics/btq224
Parallelization of the MAFFT multiple sequence alignment program
resolves10.1093/molbev/msq140
The Impact of rRNA Secondary Structure Consideration in Alignment and Tree Reconstruction: Simulated Data and a Case Study on the Phylogeny of Hexapods
resolves10.1093/bioinformatics/bts198
Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm
resolves10.1186/1471-2105-11-538
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree
resolves10.1016/j.funeco.2010.05.002
An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology
resolves10.1093/bioinformatics/14.5.407
COFFEE: an objective function for multiple sequence alignments.
resolves10.1186/1471-2105-7-471
The accuracy of several multiple sequence alignment programs for proteins
resolves10.1016/j.jmb.2004.04.058
3DCoffee: Combining Protein Sequences and Structures within Multiple Sequence Alignments
resolves10.1186/1471-2105-12-S1-S38
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach
resolves10.1038/msb.2011.75
Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
resolves10.1093/nar/gkp885
PROSITE, a protein domain database for functional characterization and annotation
resolves10.1186/1471-2105-8-116
ASH structure alignment package: Sensitivity and selectivity in domain classification
resolves10.1002/prot.20211
Detecting local structural similarity in proteins by maximizing number of equivalent residues
resolves10.1093/nar/22.22.4673
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
resolves10.1093/bioinformatics/btp033
Jalview Version 2—a multiple sequence alignment editor and analysis workbench
The 1 reference without a DOI — listed, not checked
no DOI — not checked32_44318517
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