MacClade protocols

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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Maintainer


  • person_outline MacClade Team <>

Publication for MacClade

MacClade IN pipelines

 (10)
2013
PMCID: 3724901
PMID: 23922810
DOI: 10.1371/journal.pone.0069814

[…] independently and datasets were partitioned in the phylogenetic analyses (described below)., both the trnl-f and its sequence datasets were aligned in clustalx 2.0 [40] and manually checked in macclade 4.08a [41]. sites of ambiguous homology and indels were excluded from analyses. models of nucleotide substitution for all molecular markers were estimated in jmodeltest 0.1.1 [42] […]

2013
PMCID: 3747208
PMID: 23977079
DOI: 10.1371/journal.pone.0071577

[…] (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: 3280448
PMID: 22334516
DOI: 10.1128/mBio.00240-11

[…] differences (p distance) were calculated using the seqpdist function in matlab. alignments of sequences with large p distances (many nucleotide comparisons differed) were manually verified in macclade., to examine evidence of selection on genes or regions of the genome, the ratio of the number of nonsynonymous substitutions to the number of synonymous substitutions (dn/ds ratio) […]

2012
PMCID: 3493392
PMID: 23145200
DOI: 10.1371/journal.pntd.0001882

[…] from laboratory passaged worms or previously published data. therefore, these data were only analyzed at a basic phylogenetic level and not the population level. the nad1 haplotypes were aligned in macclade v4.05 and exported into mega v5 [25]. evolutionary relationships between the haplotypes were inferred using the neighbour-joining method and 1000 bootstraps to test the reliability […]

2012
PMCID: 3862518
PMID: 24533313
DOI: 10.1016/j.ijppaw.2012.11.001

[…] 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 […]

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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