Protocol detail

Multivariate Analysis of Molecular Fingerprints

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Principal component analysis (PCA) and multi-dimensional scaling (MDS) were used as alternative grouping methods, producing three-dimensional plots in which the entries were spread according to their relatedness. Dimensioning techniques were executed with AFLP data after conversion into a band matching table. Automated band matching was performed on all fingerprint entries within the comparison, considering minimum profiling of 5%, with the optimization and position tolerances for selecting bands set to 0.10%. Default settings were applied for PCA and MDS in BioNumerics v7.6, subtracting the average for characters [38 (link)]. All Figs were exported and treated using Corel Draw X8.

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de Carvalho J.A., Hagen F., Fisher M.C., de Camargo Z.P, & Rodrigues A.M. (2020). Genome-wide mapping using new AFLP markers to explore intraspecific variation among pathogenic Sporothrix species. PLoS Neglected Tropical Diseases, 14(7), e0008330.

Publication 2020

Corel Draw X8

Characters Figs Tolerances

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Protocol cited in 1 other protocol

Variable analysis

independent variables

Dimensioning techniques (PCA and MDS)

dependent variables

Relatedness/grouping of entries in three-dimensional plots

control variables

Minimum profiling of 5%
Optimization and position tolerances for selecting bands set to 0.10%
Default settings for PCA and MDS in BioNumerics v7.6
Subtracting the average for characters

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