src/main/resources/prottest.properties | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 follow a hint from upstream how to uses system wide installed phyml

build.xml | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 build using debian packaged jars

src/main/java/es/uvigo/darwin/prottest/util/fileio/AlignmentReader.java | 8 4 + 4 - 0 !
1 file changed, 4 insertions(+), 4 deletions(-)

 alter import

src/main/java/es/uvigo/darwin/prottest/exe/PhyMLv3AminoAcidRunEstimator.java | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 properly resolve stats and tree files, add missing dot