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 hg38 the following query assemblies were affected:
	HLapoSpe1
	HLcarSowe1A
	HLcasYok2B
	HLcheLug1
	HLcheReg1
	HLchiIsr1
	HLcolGue1
	HLcorRaf1
	HLcunPaca1
	HLdesRot12A
	HLdesRot12B
	HLescRob3
	HLgeoBur1
	HLglaVol1
	HLhapAlao1
	HLmanSph3
	HLmicOre1
	HLmunCri2
	HLmyoCal2
	HLnycThe1B
	HLodoHem2
	HLpagLar1
	HLpenLuca1A
	HLpitPit2
	HLpleAur1
	HLpusHisBot1
	HLsaiSci1
	HLzalCali2
	calJac4
for reference assembly mm10 the following query assemblies were affected:
	HLartLitu2B
	HLateCha1
	HLcasYok1B
	HLcerAlb1
	HLeulCoro1
	HLgalSen1
	HLictTrid4A
	HLictTrid4B
	HLlepYar1
	HLmerPsa1
	HLmesBid2B
	HLmirCoq2
	HLmyoEma1B
	HLmyoLuc2
	HLmyoMys2B
	HLmyoNat1A
	HLneoFus1
	HLotoCra2
	HLpagLar1
	HLpipAbr1
	HLpipJav1
	HLplaHell1B
	HLpseFum1
	HLpteAle1A
	HLrhiPum1A
	HLrhyPet1A
	HLscoKuh1
	HLtapIndi3A
	HLtapIndi3B
	HLtokOsi1
	HLtupChi2
	HLtylFul1
	HLuroPar2A
	HLursAme3
	HLxanPyg1
for reference assembly HLbosTau10 the following query assemblies were affected:
	HLariCup2A
	HLartInt1B
	HLcapSib1
	HLcarPer3
	HLcatWag1
	HLdicSum1
	HLdicSumHar2
	HLequAsin4
	HLeryPat3
	HLeubGla2
	HLgarKeen1A
	HLgloCom1A
	HLhipAmp3
	HLhooLeu1
	HLictTrid4A
	HLlepYer2A
	HLlopEvot1A
	HLmacFas7
	HLmegLyr2
	HLmegNova3
	HLmesSte1
	HLmicCal1A
	HLmicGri1
	HLmicPen1A
	HLminAus1
	HLminNat2B
	HLmopPli1
	HLmusNiv1
	HLmyoBoc1
	HLmyoEma1A
	HLneoNeb2
	HLneoShe1
	HLokaJoh2
	HLotaByr1
	HLphyCat2
	HLpleAur1
	HLpteGig1
	HLpteParMex3
	HLpteVam3
	HLratRat7
	HLrhiHip1A
	HLrhiPum1B
	HLrhoPar1
	HLscoTegu1
	HLspiGra1
	HLtenEcau2A
	HLtriPer1A
	HLuroTal1
	HLvarVar1
	cavApe1
for reference assembly HLeleMaxInd3A the following query assemblies were affected:
	HLailMel2
	HLaleOec1
	HLammLer1
	HLartLit1A
	HLbabCel1
	HLbalBor1
	HLbisBon1
	HLcapHir2
	HLcerEla2
	HLchiIsr1
	HLchlSab3
	HLdipSag1
	HLeliQue1A
	HLequAsin4
	HLeulCol1
	HLfelCha1
	HLhelMal1
	HLhelPar1
	HLhipArm1
	HLhipArm2
	HLhipNigNig2
	HLiaxIox1
	HLictTrid4B
	HLlopAte1
	HLlutLut1
	HLmacSil1
	HLmacWat1B
	HLmesSte1
	HLmicCal1B
	HLmolAlv2B
	HLmunMun1
	HLmunVag1
	HLmusErm1
	HLmusPutFur2
	HLmyoMys2A
	HLnanDamRuf3
	HLneoVis2
	HLotaByr1
	HLoviArie7
	HLoviNivLyd1
	HLperCri1
	HLphaAfr1
	HLpleCal1
	HLpusHisBot1
	HLrhiAff4
	HLrhyNas2A
	HLsagImp1
	HLsapApe3
	HLspiGra1
	HLsusScro12
	HLtamTet2
	HLtapInd1
	HLtenEcau2A
	HLtriNic1B
	HLuroPar1
	HLuroTal1