Fix ultrametricity is some bespoke files

[davidebbo]

GitHub doesn't make it very easy to grasp the diff when looking at long line, but it can be looked at in other tools (e.g. VS Code at least highlights the changes).

I used a tool-guided but still somewhat manual process to fix up a selection of files to make them ultrametric. I will get some of the tools in later, along with some tests, but this is a first step, if only for discussion.

The summary is:

• AfrotheriaPoulakakis2010.phy: change 26.110648 to 26.110649. All leaves are now at exactly 84.2
• BicherSuzuki2010.phy: had (Polypterus_bichir_bichir:0.0,Polypterus_bichir_lapradei):0.0. Added the missing :0.0 on lapradei
• GalapagosFinchesLamichhaney2015.phy: changed 0.355 to 0.364 to make all leaves exactly at 0.91 (some were before at 0.901)
• GarsDeepfin.phy: changed 16.241946 to 16.241947. All leaves now at 267.9
• PalaeognathaeMitchell2014.PHY: subtract the extinction prop on 3 species, as the lengths was clashing with rest of tree. Also adjusted a few other lengths.
• PrimatesOneZoom.phy: fixed what was very likely a typo. It had Eulemur_rufus:7.6:0, and I removed the bogus :0 at the end. This file is actually not being used, but may as well fix this.
• PrimatesSpringer2012_AT.PHY: a bunch of length adjustments, by either 1 or 2 years (e.g. 3.094355 -> 3.094356). Insignificant, but made the whole file ultrametric at exactly 65.0.
• Tetrapods_Zheng_base.PHY: fixed the 37k extra year issue we discussed.

Notes:

• There are more files to be fixed. Some are more problematic and will require discussion
• This is all separate from the discussed absolute handling of @ syntax length, which is orthogonal.

[hyanwong]

This is great. Thanks a lot for doing this @davidebbo. You have no idea how long it would have taken me to hunt those down.

[hyanwong]

Happy to merge this.

[davidebbo]

For cross reference, this change is part of the discussion in #18