Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Rothfels CJ, Li F, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart Jr. CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GK, Pryer KM

Date Published: July 22, 2015

DOI: http://dx.doi.org/10.5061/dryad.62f0r

 

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Title MrBayes_configAndResults
Description Nexus datafile (alignment), MrBayes commands, and resulting parameter and tree log files.
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Title alignments_andTrees_v5
Description Nexus files (alignments) for each locus, with their corresponding maximum likelihood tree.
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Title add_genbankNums_toVouchertable
Description Python script to extract the genBank numbers from the list supplied by NCBI (in response to a sequin submission) and format them into an accession-by-locus table.
Download add_genbankNums_toVouchertable.py (1.746 Kb)
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Title add_node_numbers_to_tree
Description Python script to print a version of an input phylogeny with the nodes annotated with their node number. (So that, e.g., the nodes can be matched to their divergence time estimates, etc.)
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Title append_metadata_tofasta_forSequin
Description A python script that goes through a single-locus alignment and matches each taxon in that alignment with the corresponding metadata, which it adds in a Sequin block to the alignment file. For automating the production of Sequin submission to GenBank in cases where there are many loci, each with different combinations of taxa.
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Title nexusToNewick
Description Python script to convert a bunch of tree files from nexus to newick format.
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Title summarizing_support
Downloaded 1 time
Description R script to summarize support values across analyses. Computes average node support, does t- and z-tests to examine whether average support differs across analyses/whether support for particular nodes differs.
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When using this data, please cite the original publication:

Rothfels CJ, Li F, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart Jr. CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GK, Pryer KM (2015) The evolutionary history of ferns inferred from 25 low-copy nuclear genes. American Journal of Botany 102(7): 1089-1107. http://dx.doi.org/10.3732/ajb.1500089

Additionally, please cite the Dryad data package:

Rothfels CJ, Li F, Sigel EM, Huiet L, Larsson A, Burge DO, Ruhsam M, Deyholos M, Soltis DE, Stewart Jr. CN, Shaw SW, Pokorny L, Chen T, dePamphilis C, DeGironimo L, Chen L, Wei X, Sun X, Korall P, Stevenson DW, Graham SW, Wong GK, Pryer KM (2015) Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.62f0r
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