--- /tmp/tree-puzzle-5.3~rc16+dfsg-8ewbbj5p4/debian/tree-puzzle-doc_5.3~rc16+dfsg-8_all.deb +++ tree-puzzle-doc_5.3~rc16+dfsg-8_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2021-02-08 09:33:13.000000 debian-binary │ --rw-r--r-- 0 0 0 3948 2021-02-08 09:33:13.000000 control.tar.xz │ --rw-r--r-- 0 0 0 428320 2021-02-08 09:33:13.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 3932 2021-02-08 09:33:13.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 428264 2021-02-08 09:33:13.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ ├── data.tar.xz │ ├── data.tar │ │ ├── ./usr/share/doc/tree-puzzle/examples/tests/qp-hky-rhet-clock-nucl.nucl.puzzle │ │ │ @@ -320,18 +320,18 @@ │ │ │ : │ │ │ :-----1 Thylacinus │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889 │ │ │ Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510 │ │ │ -Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178 │ │ │ +Dasyurus 3 0.00001 0.00399 11 0.07879 0.07178 │ │ │ Echymipera 4 0.20360 0.08378 │ │ │ Trichosuru 5 0.15345 0.07805 │ │ │ -Phalanger 6 0.18858 0.08736 │ │ │ +Phalanger 6 0.18858 0.08737 │ │ │ Philander 7 0.16082 0.07443 10 iterations until convergence │ │ │ Bos 8 0.30632 0.12025 log L: -569.50 │ │ │ │ │ │ WARNING --- at least one branch length is close to an internal boundary! │ │ │ │ │ │ │ │ │ Consensus tree with maximum likelihood branch lengths │ │ ├── ./usr/share/doc/tree-puzzle/examples/tests/qp-hky-rhet-nucl.nucl.puzzle │ │ │ @@ -320,18 +320,18 @@ │ │ │ : │ │ │ :-----1 Thylacinus │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ Thylacinus 1 0.13266 0.07077 9 0.14146 0.08889 │ │ │ Sarcophilu 2 0.16398 0.05399 10 0.15536 0.07510 │ │ │ -Dasyurus 3 0.00001 0.00141 11 0.07879 0.07178 │ │ │ +Dasyurus 3 0.00001 0.00399 11 0.07879 0.07178 │ │ │ Echymipera 4 0.20360 0.08378 │ │ │ Trichosuru 5 0.15345 0.07805 │ │ │ -Phalanger 6 0.18858 0.08736 │ │ │ +Phalanger 6 0.18858 0.08737 │ │ │ Philander 7 0.16082 0.07443 10 iterations until convergence │ │ │ Bos 8 0.30632 0.12025 log L: -569.50 │ │ │ │ │ │ WARNING --- at least one branch length is close to an internal boundary! │ │ │ │ │ │ │ │ │ Consensus tree with maximum likelihood branch lengths │ │ ├── ./usr/share/doc/tree-puzzle/examples/tests/ut-pure-prot.trees.clean │ │ │ @@ -171,15 +171,15 @@ │ │ │ : :-----------------7 LGB2_LUPLU │ │ │ : │ │ │ :-1 HBB_HUMAN │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ HBB_HUMAN 1 0.04 0.03 8 0.28 0.08 │ │ │ -HBB_HORSE 2 0.12 0.03 9 0.00 0.00 │ │ │ +HBB_HORSE 2 0.12 0.03 9 0.00 9.00 │ │ │ HBA_HUMAN 3 0.02 0.02 10 0.40 0.12 │ │ │ HBA_HORSE 4 0.09 0.03 11 0.60 0.11 │ │ │ MYG_PHYCA 5 1.33 0.21 │ │ │ GLB5_PETMA 6 0.70 0.14 9 iterations until convergence │ │ │ LGB2_LUPLU 7 1.76 0.28 log L: -1699.50 │ │ │ │ │ │ WARNING --- at least one branch length is close to an internal boundary! │ │ ├── ./usr/share/doc/tree-puzzle/examples/tests/ut-pure-prot.trees.puzzle │ │ │ @@ -171,15 +171,15 @@ │ │ │ : :-----------------7 LGB2_LUPLU │ │ │ : │ │ │ :-1 HBB_HUMAN │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ HBB_HUMAN 1 0.04834 0.03148 8 0.28039 0.08746 │ │ │ -HBB_HORSE 2 0.12686 0.03876 9 0.00001 0.00100 │ │ │ +HBB_HORSE 2 0.12686 0.03876 9 0.00001 9.00000 │ │ │ HBA_HUMAN 3 0.02653 0.02208 10 0.40361 0.12824 │ │ │ HBA_HORSE 4 0.09440 0.03145 11 0.60481 0.11282 │ │ │ MYG_PHYCA 5 1.33106 0.21114 │ │ │ GLB5_PETMA 6 0.70107 0.14140 9 iterations until convergence │ │ │ LGB2_LUPLU 7 1.76830 0.28198 log L: -1699.50 │ │ │ │ │ │ WARNING --- at least one branch length is close to an internal boundary! │ │ │ @@ -251,15 +251,15 @@ │ │ │ : :-------6 GLB5_PETMA │ │ │ : │ │ │ :-1 HBB_HUMAN │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ HBB_HUMAN 1 0.04869 0.03153 8 0.27871 0.08717 │ │ │ -HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15661 │ │ │ +HBB_HORSE 2 0.12653 0.03874 9 0.12334 0.15660 │ │ │ HBA_HUMAN 3 0.02634 0.02204 10 0.39110 0.12780 │ │ │ HBA_HORSE 4 0.09459 0.03147 11 0.60627 0.11286 │ │ │ MYG_PHYCA 5 1.22880 0.20960 │ │ │ GLB5_PETMA 6 0.69972 0.14141 11 iterations until convergence │ │ │ LGB2_LUPLU 7 1.68480 0.28106 log L: -1699.32 │ │ │ │ │ │ │ │ │ @@ -291,15 +291,15 @@ │ │ │ : │ │ │ :-1 HBB_HUMAN │ │ │ │ │ │ │ │ │ branch length S.E. branch length S.E. │ │ │ HBB_HUMAN 1 0.04834 0.03148 8 0.40364 0.12824 │ │ │ HBB_HORSE 2 0.12685 0.03876 9 0.28040 0.08746 │ │ │ -HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11281 │ │ │ +HBA_HUMAN 3 0.02653 0.02208 10 0.60481 0.11282 │ │ │ HBA_HORSE 4 0.09440 0.03145 │ │ │ MYG_PHYCA 5 1.33095 0.21112 │ │ │ GLB5_PETMA 6 0.70107 0.14140 10 iterations until convergence │ │ │ LGB2_LUPLU 7 1.76831 0.28198 log L: -1699.50 │ │ │ │ │ │ │ │ │ Unrooted user defined tree with maximum likelihood branch lengths