I wrote a very ugly Bash script that should do what you want (not tested at all, assumes there are no spaces in names and names are separated from the alignments by a single space). Name it e.g. trimEnds.sh, then chmod +x trimEnds.sh and use it by ./trimEnds.sh alignmentFile

#!/bin/bash
#separate the alignment from the names
cut -f2 -d " " $1 > $1.ali
cut -f1 -d " " $1 > $1.names

#Set start at 1
START=1

#Set end at alignment length
END=$(head -n1 $1.ali | awk '{print length}')

#Find out where the good stuff starts
for (( i=$START; i<=$END; i++ ))
    do
    nonLetterCount=$(cut -c$i $1.ali | tr -d [A,T,G,C] | grep . | grep -c .)
    if [ "$nonLetterCount" -gt "0" ]
        then
        (( START = $i + 1 ))
    else
        break
    fi
    done

#Find out where the good stuff ends
for (( i=$END; i>=$START; i-- ))
        do
    nonLetterCount=$(cut -c$i $1.ali | tr -d [A,T,G,C] | grep . | grep -c .)
        if [ "$nonLetterCount" -gt "0" ]
                then
                (( END = $i - 1 ))
        else
                break
        fi
    done

#Reunite names with seqs
paste -d " " $1.names <(cut -c$START-$END $1.ali) > $1.mod

#Remove unnecessary files
rm $1.names $1.ali