Computational protocol: Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid

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Protocol publication

[…] Sequences were aligned using the MAFFT (Multiple Alignment using Fast Fourier Transform) web server at the European Bioinformatics Institute []. Default parameters were used: gap opening penalty = 1.53, gap extension penalty = 0.123, tree rebuilding number = 1, maxiterate = 0, and perform FFTS = localpair. The sequence alignment is available as a supplementary FASTA file (Additional file ).Within-species 5S-NTS polymorphism was estimated, based on the aforementioned multiple alignment, using DnaSP version 5.10.01 []. The relationship between numbers of polymorphic sites and minimum numbers of visible 5S rDNA signals was investigated using linear regression analysis (in Microsoft Excel).Phylogenetic reconstruction was performed using maximum likelihood optimization available through the RaxML BlackBox web server [] running RaxML version 7.2.8 []. Default settings were used. The 8 Phragmipedium besseae sequences were indicated as the outgroup. RaxML was called using the following commands: raxml -# 100 -n pasted -o bess1, bess2, bess3, bess4, bess5, bess6, bess7, bess8 -f a -m GTRGAMMA -x 564547904 -p 564547904 -s 0VaDTW. All search information, as was output on the web site, is included in Additional file . […]

Pipeline specifications

Software tools MAFFT, DnaSP, RAxML
Application Phylogenetics