bbabbd5d2566d47d923d51dbe350634783455999
mspeir
  Sun Oct 26 12:14:52 2025 -0700
change soe to gi, refs #35031

diff --git src/hg/htdocs/Neandertal/index.html src/hg/htdocs/Neandertal/index.html
index 79a9a92942c..51aba156355 100755
--- src/hg/htdocs/Neandertal/index.html
+++ src/hg/htdocs/Neandertal/index.html
@@ -39,31 +39,31 @@
                         Blat</A><HR>
                     <A CLASS="leftbar" HREF="../cgi-bin/hgTables">
                         Table Browser</A><HR>
                     <A CLASS="leftbar" HREF="../cgi-bin/hgNear">
                         Gene Sorter</A><HR>
                     <A CLASS="leftbar" HREF="../cgi-bin/hgPcr">
                         In Silico PCR</A><HR>
                     <A CLASS="leftbar" HREF="../cgi-bin/hgGenome">
                         Genome Graphs</A><HR>
                     <A CLASS="leftbar" HREF="http://galaxy.psu.edu"
 			TARGET=_blank>Galaxy</A><HR>
                     <A CLASS="leftbar" HREF="../cgi-bin/hgVisiGene">
                         VisiGene</A><HR>
                     <A CLASS="leftbar" HREF="../util.html">
                         Utilities</A><HR>
-                    <A CLASS="leftbar" HREF="http://hgdownload.soe.ucsc.edu/downloads.html">
+                    <A CLASS="leftbar" HREF="http://hgdownload.gi.ucsc.edu/downloads.html">
                         Downloads</A><HR>
                     <A CLASS="leftbar" HREF="../goldenPath/releaseLog.html">
                         Release Log</A><HR>
                     <A CLASS="leftbar" HREF="../goldenPath/customTracks/custTracks.html">
                         Custom Tracks</A><HR>
                     <A CLASS="leftbar" HREF="http://microbes.ucsc.edu/">
                         Microbial Genomes</A><HR>
                     <A CLASS="leftbar" HREF="../mirror.html">
                         Mirrors</A><HR>
                     <A CLASS="leftbar" HREF="../training/index.html" TARGET=_blank>
                         Training</A><HR>
                     <A CLASS="leftbar" HREF="../goldenPath/credits.html">
                         Credits</A><HR>
                     <A CLASS="leftbar" HREF="../goldenPath/pubs.html">
                         Publications</A><HR>
@@ -283,259 +283,259 @@
 TARGET=_BLANK>samtools</A> and 
 <A HREF="http://picard.sourceforge.net/"
 TARGET=_BLANK>PICARD</A> are useful for viewing and manipulating BAM 
 files.
 
 The .bw suffix denotes the 
 <A HREF="../goldenPath/help/bigWig.html">bigWig</A> format, which stores 
 a numeric signal for genomic positions.</P>
 <P>
 All links below can be fetched using 
 <A HREF="http://rsync.samba.org/" TARGET=_BLANK>rsync</A>; replace 
 &quot;ftp://&quot; with &quot;rsync://&quot; in the links below.
 <UL>
 <LI><B>Neandertal Alleles in Human/Chimp Coding Non-synonymous Differences in Human Lineage:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntHumChimpCodingDiff.txt.gz</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntHumChimpCodingDiff.txt.gz</A><BR>
 </LI>
 <LI><B>Selective Sweep Scan (S) on Neandertal vs. Human Polymorphisms:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/bbi/ntSssZScorePMVar.bw</A><BR>
 </LI>
 <LI><B>Selective Sweep Scan (S): 5% Smallest S scores:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssTop5p.txt.gz</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssTop5p.txt.gz</A><BR>
 </LI>
 <LI><B>SNPS Used for Selective Sweep Scan (S):</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssSnps.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntSssSnps.txt.gz</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssSnps.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntSssSnps.txt.gz</A><BR>
 </LI>
 <LI><B>Candidate Regions for Gene Flow from Neandertal to Non-African Modern Humans:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntOoaHaplo.txt.gz</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntOoaHaplo.txt.gz</A><BR>
 </LI>
 <LI><B>Neandertal Sequence Contigs Generated by Genotype Caller:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/all-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Feld1-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Mez1-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Sid1253-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.16-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.25-hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/Vi33.26-hg18.bam.bai</A><BR>
 Chimpanzee (panTro2):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/all-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Feld1-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Mez1-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Sid1253-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.16-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.25-pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/Vi33.26-pt2.bam.bai</A><BR>
 </LI>
 <LI><B>Neandertal Sequence Reads:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLFeld1.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLMez1.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLSid1253.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.16.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.25.hg18.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/seqAlis/SLVi33.26.hg18.bam.bai</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLFeld1.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLMez1.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLSid1253.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.16.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.25.hg19.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/seqAlis/SLVi33.26.hg19.bam.bai</A><BR>
 Chimpanzee (panTro2):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLFeld1.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLMez1.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLSid1253.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.16.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.25.pt2.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/panTro2/neandertal/seqAlis/SLVi33.26.pt2.bam.bai</A><BR>
 </LI>
 <LI><B>Alignments of Sequence Reads from 5 Modern Humans:</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS4_HGDP00778_Han.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS5_HGDP00542_Papuan.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS6_HGDP00927_Yoruba.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS7_HGDP01029_San.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/humans/MMS8_HGDP00521_French.paired.qualfilt.rmdup.entropy1.0.sort.bam.bai</A><BR>
 </LI>
 <LI><B>Neandertal Mitochondrial Sequence (2008):</B><BR>
 Human (hg18):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntMito.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntMito.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg18/database/ntMito.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg18/neandertal/ntMito/ntM.fa</A><BR>
 Human (hg19):<BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.sql"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.sql</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz"
->ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz</A><BR>
-<A HREF="ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa"
->ftp://hgdownload.soe.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntMito.sql"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntMito.sql</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz"
+>ftp://hgdownload.gi.ucsc.edu/goldenPath/hg19/database/ntMito.txt.gz</A><BR>
+<A HREF="ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa"
+>ftp://hgdownload.gi.ucsc.edu/gbdb/hg19/neandertal/ntMito/ntM.fa</A><BR>
 </LI>
 </UL>
 </P>
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