These files describe the datasets used for the paper "An empirical
evaluation of phylogenetic strategies using a multilocus dataset from
North American pines" by M DeGiorgio et al. (BMC Evol Biol XX:XX-XX
[2014]).

Michael DeGiorgio
January 16, 2014
mxd60@psu.edu

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Legend:

Short code    Long code         Species name
----------    --------------    --------------- 
PIAL          P_albicaulis      P. albicaulis
PIAY          P_ayacahuite      P. ayacahuite
PIFL          P_flexilis        P. flexilis
PILA          P_lambertiana     P. lambertiana
PIMN          P_monticola       P. monticola	
PISB          P_strobiformis    P. strobiformis	
PIST          P_strobus	        P. strobus
PICH          P_chiapensis      P. chiapensis	
PIGE          P_geradiana       P. geradiana
PIBU          P_bungeana        P. bungeana
PISQ          P_squamata        P. squamata

Each individual among the 120 individuals considered by DeGiorgio et
al. is given the same name in all files in which the individual appears.

A total of 121 loci were in the full dataset D_p. The dataset D_s also
contains 121 loci, but with one sequence per species. Datasets D_{p,0}
and D_{s,0} enforce a sequence difference constraint for inclusion of
a locus, and therefore have fewer than 121 loci.

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1. Directory Dataset_Dp

This folder includes the full dataset used by DeGiorgio et
al. (2014). Each folder contains a list of files, where the file name
is the name of a particular sequenced genetic locus. Each file is in
FASTA format. Each sequence is represented by a pair of consecutive
lines, with the first line being the sequence name and the second line
being the sequence. The species to which an individual sequence
belongs is denoted by a substring chosen from among the short codes above.

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2. Directory Dataset_Dp0

This folder includes the D_{p,0} dataset used by DeGiorgio et
al. (2014). Each folder contains a list of files, where the file name
is the name of a particular sequenced genetic locus. Each file is in
FASTA format. Each sequence is represented by a pair of consecutive
lines, with the first line being the sequence name and the second line
being the sequence. The species to which an individual sequence
belongs is denoted by a substring chosen from among the short codes above.

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3. Directory Dataset_Ds

This folder includes the D_s dataset used by DeGiorgio et
al. (2014). Each folder contains a list of files, where the file name
is the name of a particular sequenced genetic locus. Each file
contains 11 lines, where each line is one of the 11 species (eight
ingroup and three outgroup) considered in the study. Each line is
formatted with the species' long code followed by a tab and then the
sequence for that species.

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4. Directory Dataset_Ds0

This folder includes the D_{s,0} dataset used by DeGiorgio et
al. (2014). Each folder contains a list of files, where the file name
is the name of a particular sequenced genetic locus. Each file
contains 11 lines, where each line is one of the 11 species (eight
ingroup and three outgroup) considered in the study. Each line is
formatted with the species' long code followed by a tab and then the
sequence for that species.

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