MacClade specifications

Information


Unique identifier OMICS_16524
Name MacClade
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Mac OS
Computer skills Medium
Version 4.08
Stability Stable
Maintained Yes

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  • person_outline MacClade Team <>

MacClade article

MacClade citations

 (5)
2014
PMCID: 4021497

[…] sequenced, which ultimately yielded a sample of 84 sequenced isolates (additional file 1: table s1)., sequences were aligned using mafft [116] with default parameters. genotypes were identified in macclade 4.05 [117]. some portions of the its included indels and these regions were removed from the analysis., specialization is most easily quantified as the number of taxa with which a taxon […]

2013
PMCID: 3747208

[…] (macrogen, seoul, korea)., the original sequences were edited and aligned using clustalw multiple alignment option within the software bioedit [65]. reading frame errors were checked in the software macclade v. 4.07 [66]. in addition, the coi sequences of a. taeniatus and a. zebra from genbank were incorporated to the data matrix. additionally, sequences from two related galaxiids species [2] […]

2012
PMCID: 3862518

[…] et al., 2003). sequences were aligned by eye to a previously assembled alignment of ssrdna and lsrdna (olson et al., 2003) which included renicola sp. and tanaisia fedtschenkoi (eucotylidae), using macclade (maddison and maddison, 2005). a published sequence of lsrdna from the eucotylid tamerlania zarudnyi (genbank accession af184248) was included in the lsrdna alignment., to extract dna […]

2007
PMCID: 1920508

[…] scanned for characteristics expected of transit peptides for the group in question., new sequences were aligned to homologues from public databases using clustal x, and manually edited using macclade 4.07. publicly available sequences used in alignments were downloaded from nr genbank, estdb, or from complete eukaryotic genome databases. all sequences found to be closely related […]

2006
PMCID: 1431560

[…] m13r primers using the dye terminator cycle sequencing method with an mj research automated sequencer., sequences were aligned using the program clustal x [83], followed by manual adjustment using macclade 4.0 [84] and bioedit sequence alignment editor [85]. non-aligned regions of length variation in v1 and v2 were removed (corresponding to nucleotides 6932–6974), and sequences containing […]

MacClade institution(s)
Department of Integrative Biology, University of California, Berkeley, CA, USA; Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
MacClade funding source(s)
Supported by a Natural Sciences and Engineering Council of Canada Postdoctoral Fellowship.

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