I analyzed the phylogeny of this haplogroup by using fully sequenced and published mtDNA data from GenBank.
To do so I first downloaded the data from GenBank, then I used CLUSTALW, (mode: slow accurate pairwise alignment) to align the sequences and create a rooted phylogenetic tree with branch length (UPGMA). The data were pasted into CLUSTALW in the Fasta format.
I realized that all the data of Herrnstadt et al. 2002 are lacking the first 577 nucleotides, which is messing up the position of Herrnstadt samples in the trees/network and is messing up the position of the rest. The same effect can be seen with the two samples of Kivisild et al.; they are lacking 236 nucleotides. Thus, I excluded these samples.
Rooted phylogenetic tree with branth length (UPGMA) of H5a1:
The nice thing about CLUSTALW is that it also generates a "dnd file" and an "aln file" of the alignment.
The dnd file can be opened with the Figtree software. In Figtree, I generated another tree of H5a1:
The aln file can be opened with the Splitstree software. In Splitstree4, I generated a network (Convex Hull) of H5a1:
H5a1b (G11719A mutation): two individuals in these trees have this mutation [AY495167(European) Coble; AY495176(European) Coble]
H5a1c1a (C4095T G13194A G9055A A2851G mutations): only one individual in these trees has these mutations [HQ663878(Danish) FTDNA]
H5a1d (A8803D mutation): only one individual in these trees has this mutation [AY495171(European) Coble]
H5a1e (A16166G mutation): two individuals from Finland belong to the H5a1e branch [AY339431(Finland) Moilanen; AY339432(Finland) Moilanen].
H5a1f (T961C mutation): one individual in these trees has this mutation [ JN646689(Polish) FTDNA]
H5a1g1 (T16172C, A444G, G9804A, T16311C mutations): two individuals in these trees have these mutations [EU294323 FTDNA; HQ645111(English) FTDNA]. Since HQ645111 has the additional T1284C and A7517G mutations it belongs to H5a1g1a.
Note: In the Finland DNA project I found one individual (N48161 Mary Anne Bodle, b.1791, Plumstead, Kent) that originated in England and has the same mutations of H5a1g1 HV regions, i.e. A444G, T16172C, T16311C.
H5a1k (T12864C): two individuals have this mutation [AY495170(European) Coble, GQ983064(Italy) Santoro]
H5a1p (T16093C): three individuals have this mutation [FJ966912 FTDNA, GQ983075(Italy) Santoro, GQ983084(Italy) Santoro]