Thank you for using these datasets.
The files are organized as follows:

high_frag subdirectory contains the high fragmentation condition data.
low_frag subdirectory contains the low fragmentation condition data.

The next level of subdirectories are the different model conditions (e.g. 1000M1), 
each containing one or more replicates. 

Each replicate contains the following files:

LOGISTICAL:
true_align.txt          The true alignment with no fragmentation
true_align_fragged.txt  The true alignment with fragmentation
true_tree.tre           The true tree
true_unalign.txt        Unaligned sequences with no fragmentation
unaligned_all.txt       Unaligned sequences with fragmentation
unaligned_frag.txt      Unaligned fragmentary sequences
unaligned_full.txt      Unaligned full-length sequences
log.txt                 The commands that were run

RESULTS:
MSA-ML Methods
"PASTA-FastTree"        pasta.tre
"PASTA-RAXML"           pasta_raxml.tre
"UPP(F)-FastTree"       pasta_upp_fasttree.tre
"UPP(F)-RAXML"          pasta_upp_raxml.tre
"UPP(R)-FastTree"       pasta_raxml_upp_fasttree.tre
"UPP(R)-RAXML"          pasta_raxml_upp_raxml.tre
    
PLACEMENT Methods
"UPP(F)-pplacer"        pasta_upp_pplacer.tre
"SEPP(F)-pplacer"       pasta_sepp_pplacer.tre
"SEPP(F)-pplacer(c)"    pasta_sepp.tre
"UPP(F)-APPLES"         pasta_upp_apples.tre          
"UPP(R)-pplacer"        pasta_raxml_upp_pplacer.tre
"SEPP(R)-pplacer"       pasta_raxml_sepp_pplacer.tre
"SEPP(R)-pplacer(c)"    pasta_raxml_sepp.tre
"UPP(R)-APPLES"         pasta_raxml_upp_apples.tre