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Pipeline publication

[…] b' minimum length of a block was set to 5. C) The parameter for the allowed gap position was set to \xe2\x80\x98with half\xe2\x80\x99 meaning that only positions within 50% or more of the sequences having a gap are treated as gap positions. In addition, datasets excluding the amoebozoan lamins, both the Oikopleura dioica and a set of Platyhelminth lamins, or all these lamins were generated to investigate branch attraction effects between these sequences. Finally, datasets were created, in which highly variable regions were removed manually., Phylogenetic trees were generated using the Neighbour Joining (1) and the Maximum likelihood (2) method. 1. Unrooted trees with 1,000 bootstrap replicates were calculated with ClustalW v.2.0.10. Trees were corrected for multiple substitutions. 2. FastTree v.2 was used to perform Maximum likelihood (ML) analyses with estimated proportion of invariable sites and bootstrapping (1,000 replicates). FastTree offers the JTT and WAG amino acid substitution models. The more appropriate model was determined by using ProtTest v.3.2 calculating the tree topology with the BioNJ algorithm and optimizing both the branch lengths and the model of protein evolution simultaneously. According to the Akaike Information Criterion (AIC), the JTT+\xce\x93 was determined to be the best model. Phylogenetic trees were visualized with FigTree ( http://tree.bio.ed.ac.uk/software/figtree/)., How to cite this article: Kollmar, M. Polyphyly of nuclear lamin genes indicates an early eukaryotic origin of the metazoan-type intermediate filament proteins. Sci. Rep. 5, 10652; doi: 10.1038/srep10652 (2015)., It was a pleasure for me to have stimulating discussions with Klaus Weber about phylogenetic, cell biological and lamin-related topics over many years.]' […]

Pipeline specifications

Software tools Clustal W, FastTree, ProtTest, FigTree