In Dec 2025, we noticed that a few whole genome alignments have been missing certain local alignments in the alignment chains. This can affect the TOGA runs and increase the number of missing genes.
We therefore recomputed the chains and re-ran TOGA2 for the following species:

for reference assembly HLgalGal7 the following query assemblies were affected:
	HLacrAru2
	HLansAnse1A
	HLansCygn3
	HLbutVir1
	HLchrAmhe1
	HLfalChe2
	HLhalPel1
	HLpeuTae1
	HLpipFil1
	HLrhyJuba2
	HLtaeGutt6
	HLzonLeu1
	HLzosHyp1
for reference assembly HLtaeGut5 the following query assemblies were affected:
	HLaraAra1
	HLathNoct1A
	HLcalBor2
	HLcasCas2
	HLcolJanNit1
	HLcorCor2
	HLeudEleg2A
	HLgraVar1
	HLmorBass1B
	HLpluApr1
	HLpodStr1
	HLsarPapa1A
for reference assembly HLcorHaw3 the following query assemblies were affected:
	HLcepGry1
	HLchrRidi2
	HLgraPic1
	HLherCac1
	HLneoBou1
	HLoxyJam1
	HLpipChl1
	HLsagSer1
	HLsphHum1
	HLxipEle1
	cotJap2
for reference assembly HLdroNov3 the following query assemblies were affected:
	HLammCau1
	HLanaAcu1
	HLcatFus1
	HLcenUro1
	HLeudSch1
	HLgruGru1A
	HLlatDis1A
	HLmalCya1
	HLnesAcu1
	HLpoeAtri2A
	HLpyrLep1
	HLstiNae1
for reference assembly HLrisTri2 the following query assemblies were affected:
	HLagaRos1
	HLbraCana2
	HLcalBore3A
	HLcenUni1
	HLclaHyem1
	HLfalChe2
	HLgeoCal1
	HLhelExor1A
	HLireCya1
	HLmolAen1
	HLpasSand2
	HLpavMut1
	HLphaNut2A
	HLphyTro1
	HLpyrRuf1
	HLstrDec1A
	HLsylAtr1
	HLsylBor1