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Felsenstein's PHYLIP package of molecular phylogeny tools has been used globally since 1980. The programs are receiving renewed attention because of their character-based user interface, which has the advantage of being scriptable for use with large-scale data studies based on super-computers or massively parallel computing clusters. However, occasionally we found, the PHYLIP Consense program output text file displays two or more divided bootstrap values for the same cluster in its result table, and when this happens the output Newick tree file incorrectly assigns only the last value to that cluster that disturbs correct estimation of a consensus tree. We ascertained the cause of this aberrant behavior in the bootstrapping calculation. Our rewrite of the Consense program source code outputs bootstrap values, without redundancy, in its result table, and a Newick tree file with appropriate, corresponding bootstrap values. Furthermore, we developed an add-on program and shell script, add_bootstrap.pl and fasta2tre_bs.bsh, to generate a Newick tree containing the topology and branch lengths inferred from the original data along with valid bootstrap values, and to actualize the automated inference of a phylogenetic tree containing the originally inferred topology and branch lengths with bootstrap values, from multiple unaligned sequences, respectively. These programs can be downloaded at: https://github.com/ShimadaMK/PHYLIP_enhance/.

Eight Argonne premium coals and an Australian brown coal (Morwell) were extracted in a flowing stream of either tetralin or 1-methylnaphthalene under 10 MPa at 200–400°C to examine the dissolution/depolymerization behavior of coal in liquid phase. The flowing solvent was used to minimize the secondary interaction between the extract and the macromolecular network of coal. Four bituminous coals were extracted with negligible decomposition below 350°C. The extract yield reached 65–80% for the bituminous coals at 350°C, and the extract was separated into about 25–40% of soluble fraction at room temperature (soluble) and about 40% of solid precipitated at room temperature (deposit). The detailed analyses of the soluble, the deposit and the residue through ultimate analysis, 13 C solid NMR, GPC, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) enabled to examine the structure of Pittsburgh #8 (PITT) in detail. The raw PITT coal was found to contain small molecules ( M W =130–600) and large molecules ( M W =1300–3500) in its network. The soluble consisted of only small molecules, but both small and large molecules were involved in the deposit and the residue. The extraction method employed in this work was found to be effective to separate coal into different molecule size fractions without decomposition for bituminous coals. The soluble, being obtained in 20–40% yield and consisting of molecules smaller than 600 of M W , and the deposit, being obtained in 40% yield at maximum and containing little ash, would be well utilized as either clean fuel or raw materials for the subsequent conversion.