MacClade protocols

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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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Publication for MacClade

MacClade in pipelines

 (36)
2017
PMCID: 5465370
PMID: 28580942
DOI: 10.1038/ncomms15740

[…] to obtain individual env sequences that proportionately represent those virions circulating in vivo., all sequence alignments and phylogenetic trees were performed in clustalw with manual editing in macclade. each low-diversity lineage was compared with a mathematical model of viral diversification overtime to identify all transmitted/founder lineages, as previously described in ref. . […]

2016
PMCID: 4743939
PMID: 26849226
DOI: 10.1371/journal.pone.0148934

[…] signed gene pairs in three or more genomes were coded as binary characters using mesquite 3.04 []. losses of ancestral gene pairs were identified by tracing these characters on tree topologies with macclade 4.08 [] under the dollo principle of parsimony., the genbank accession numbers of the 71chloroplast genomes that were used to generate the analyzed amino acid and nucleotide data sets […]

2016
PMCID: 5214745
PMID: 28070297
DOI: 10.1002/ece3.2599

[…] alignments were performed with the online version of mafft v.6.0 (katoh & toh, ). because there was little difference between l‐ins‐i strategy and q‐ins‐i strategy, we chose the former one. macclade v.4.06 (maddison & maddison, ) was used to check for premature stop codons in protein‐coding genes. we used the online version of gblocks v.0.91b (castresana, ) to identify positions […]

2016
PMCID: 5082654
PMID: 27783687
DOI: 10.1371/journal.pone.0164248

[…] codes corporation, ann arbor, mi usa). sequences were aligned by eye in sequencher 4.7 (gene codes corporation), and the number of haplotypes was determined using the filter redundant taxa option in macclade 4.08 []. golden eagle haplotypes from other studies in north america [,] were downloaded from genbank (www.ncbi.nlm.nih.gov/genbank/)., the number of alleles, observed and expected […]

2015
PMCID: 4361788
PMID: 25829846
DOI: 10.3897/zookeys.484.8363

[…] warrington, england). raw sequence chromatograms were edited using sequencher™ v. 4.8 (genes codes corporation, ann arbor, mi), aligned automatically in mafft v. 7 (its2) () or manually (coi) using macclade v. 4.06 (). sequence similarities were compared with those available (october 14, 2014) in genbank using basic local alignment search tool (blast) (http://blast.ncbi.nlm.nih.gov/blast.cgi) […]


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MacClade in publications

 (403)
PMCID: 5904484
PMID: 29674920
DOI: 10.3897/zookeys.749.23165

[…] and sequencing procedures were performed as in . all sequences were deposited in genbank, and the accession numbers are provided in table ., raw sequences were edited and assembled using macclade 4.0 (), and uncorrected pairwise distances between sequences were calculated using mega 7.0.16 () and are shown in table ., fabricius, 1775 , gammarus pulex (linnaeus, 1758), hou & li […]

PMCID: 5849365
PMID: 29494580
DOI: 10.1371/journal.pntd.0006254

[…] occurred on the internal branches of lineages formed during the evolution of denv, particularly in png, we mapped changes onto the ml phylogenetic tree using a parsimony-based method implemented in macclade 4.08 []., a serum microneutralization (mn) assay was used to measure serum anti-denv antibodies []. this approach was selected to allow simultaneous assessment of antibody to all four denv […]

PMCID: 5779762
PMID: 29504993
DOI: 10.1097/MD.0000000000009632

[…] smooth skyride plot gaussian markov random field (gmrf), nonparametric bayesian skyline plot (bsp), and implementing a relaxed molecular clock model under the conditions described above., the macclade version 4 program (sinauer associates, sunderland, ma) was used to investigate the viral gene in/out flow among distinct hav subpopulations within different geographic areas corresponding […]

PMCID: 5786241
PMID: 29325077
DOI: 10.1093/aob/mcx129

[…] dna data to be closely related to, and diverge immediately prior to, ophrys, namely steveniella, neotinea and orchis (; )., morphological data were derived from numerous sources and were input into macclade v4.05 (). when compiling our character list (), characters were, where feasible, derived from the literature and supplemented with original observations by the present authors. […]

PMCID: 5729713
PMID: 29242776
DOI: 10.5598/imafungus.2017.08.02.06

[…] ., to infer the phylogenetic placement of auritella species, we assembled separate alignments of 37 28s and 27 rpb2 dna sequences from on-going and much more taxonomically inclusive gene datasets in macclade v4.08a (), including two 28s sequences (jq657775, jq657772) produced from auritella species as “inocybe” by , and one 28s sequence (fr731774) from a caesalpinoid (fabaceae) ectomycorrhiza () […]


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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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