TY - JOUR
T1 - Concatenator, a user-friendly program to concatenate DNA sequences, implementing graphical user interfaces for MAFFT and FastTree
AU - Vences, Miguel
AU - Patmanidis, Stefanos
AU - Kharchev, Vladimir
AU - Renner, Susanne S.
N1 - Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press.
PY - 2022
Y1 - 2022
N2 - Motivation: Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning and exploring multi-gene datasets. Results: We present Concatenator, a user-friendly GUI-driven program that accepts single-marker and multi-marker DNA sequences in different input formats, including Fasta, Phylip and Nexus, and that outputs concatenated sequences as single-marker or multi-marker Fasta, interleaved nexus or Phylip files, including command files for downstream model selection in IQ-TREE. It includes the option to (re)align markers with MAFFT and produces exploratory trees with FastTree. Although tailored for medium-sized phylogenetic projects, Concatenator is able to process phylogenomic datasets of up to 30 000 markers.
AB - Motivation: Phylogenetic and phylogenomic analyses require multi-gene input files in different formats, but there are few user-friendly programs facilitating the workflow of combining, concatenating or separating, aligning and exploring multi-gene datasets. Results: We present Concatenator, a user-friendly GUI-driven program that accepts single-marker and multi-marker DNA sequences in different input formats, including Fasta, Phylip and Nexus, and that outputs concatenated sequences as single-marker or multi-marker Fasta, interleaved nexus or Phylip files, including command files for downstream model selection in IQ-TREE. It includes the option to (re)align markers with MAFFT and produces exploratory trees with FastTree. Although tailored for medium-sized phylogenetic projects, Concatenator is able to process phylogenomic datasets of up to 30 000 markers.
UR - http://www.scopus.com/inward/record.url?scp=85148557241&partnerID=8YFLogxK
U2 - 10.1093/bioadv/vbac050
DO - 10.1093/bioadv/vbac050
M3 - Article
C2 - 36699380
AN - SCOPUS:85148557241
SN - 2635-0041
VL - 2
JO - Bioinformatics Advances
JF - Bioinformatics Advances
IS - 1
M1 - vbac050
ER -