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I had this code produce the following document. I wanted to align a few things.

Particularly under the "degree sequence" heading:

documentclass[varwidth,margin=2mm]{standalone}

usepackage{amsmath,tikz}

begin{document}

    begin{center}

        begin{tikzpicture}

            %%%%% SNIP %%%%%

        end{tikzpicture}\

        rule[0cm]{200pt}{0.5pt}\

        begin{math}

            $degree sequence$\

            $e={2,2,2,2,2}            c={2,2,2,2,2}$\

            delta(e)=2                 delta(c)=2\

            Delta(e)=2                 Delta(c)=2\

            rule[0cm]{200pt}{0.5pt}\

            alpha(e_{1})=c_{1},  alpha(e_{2})=c_{3},\

            alpha(e_{3})=c_{5},  alpha(e_{4})=c_{2},\

            alpha(e_{5})=c_{4},  alpha(e_{1})=c_{1},\

            rule[0cm]{200pt}{0.5pt}\

            $e_{1}to{}e_{2}to{} e_{3}to{}e_{4}to{}

            e_{5}to{}e_{1}\

            $c_{1}to{}c_{3}to{} c_{5}to{}c_{2}to{}

            c_{4}to{}c_{1}\

            rule[0cm]{200pt}{0.5pt}\

        end{math}    

    end{center}

end{document}

So I tried to use the align package to align it, butit kind of sent everything out of wack:

documentclass[varwidth,margin=2mm]{standalone}

usepackage{amsmath,tikz}

begin{document}

    begin{center}

        begin{tikzpicture}

            %%%%% SNIP %%%%%

        end{tikzpicture}\

        rule[0cm]{200pt}{0.5pt}\

            degree sequence\

            e = {2,2,2,2,2,2} c = {2,2,2,2,2,2}\

        begin{align*}

            delta(e) & = 2 & delta(c) & = 2\

            Delta(e) & = 2 & Delta(c) & = 2\

        end{align*}

        begin{math}

            rule[0cm]{200pt}{0.5pt}\

            alpha(e_{1})=c_{1},  alpha(e_{2})=c_{3},\

            alpha(e_{3})=c_{5},  alpha(e_{4})=c_{2},\

            alpha(e_{5})=c_{4},  alpha(e_{1})=c_{1},\

            rule[0cm]{200pt}{0.5pt}\

            $e_{1}to{}e_{2}to{} e_{3}to{}e_{4}to{}

            e_{5}to{}e_{1}\

            $c_{1}to{}c_{3}to{} c_{5}to{}c_{2}to{}

            c_{4}to{}c_{1}\

            rule[0cm]{200pt}{0.5pt}\

        end{math}    

    end{center}

end{document}

Is there a way around this or am I stuck with it. I know it's only a minor thing, but it would be nice to have more control.

You want to use tabular:

documentclass[margin=6]{standalone}

usepackage{amsmath,tikz,booktabs}



begin{document}



begin{tabular}{cc}

begin{tikzpicture}

draw (0,0)--(1,1);

end{tikzpicture}

&

begin{tikzpicture}

draw (0,0)--(1,1);

end{tikzpicture}

\

midrule

multicolumn{2}{c}{degree sequence}\

$begin{aligned}

& e={2,2,2,2,2} \

& delta(e)=2 \

& Delta(e)=2 \

end{aligned}$ &

$begin{aligned}

& c={2,2,2,2,2} \

& delta(c)=2 \

& Delta(c)=2

end{aligned}$ \

midrule

multicolumn{2}{c}{%

  $begin{aligned}

  alpha(e_{1})&=c_{1}, & alpha(e_{2})&=c_{3},\

  alpha(e_{3})&=c_{5}, & alpha(e_{4})&=c_{2},\

  alpha(e_{5})&=c_{4}, & alpha(e_{1})&=c_{1},

  end{aligned}$%

} \

midrule

multicolumn{2}{c}{%

  $begin{array}{@{} c *{5}{@{} >{{}}c<{{}} @{} c @{}} }

  e_{1} & to & e_{2} & to & e_{3} & to & e_{4} & to & e_{5} & to & e_{1} \

  c_{1} & to & c_{3} & to & c_{5} & to & c_{2} & to & c_{4} & to & c_{1}

  end{array}$%

} \

bottomrule[lightrulewidth]

end{tabular}



end{document}

align and alignat allow you to align. And you can put things in a node which has the same width as the figure.

documentclass[tikz,margin=2mm]{standalone}

usetikzlibrary{positioning,calc}

usepackage{amsmath}

begin{document}

begin{tikzpicture}[Bullet/.style={circle,draw,fill=black,scale=0.75}]

begin{scope}[local bounding box=top]

begin{scope}[local bounding box=left]

 node[Bullet,label=left :{$e_1$}] (E1) at (0,2) {} ;

 node[Bullet,label=above:{$e_2$}] (E2) at (1,3) {} ;

 node[Bullet,label=right:{$e_3$}] (E3) at (2,2) {} ;

 node[Bullet,label=right:{$e_4$}] (E4) at (2,0) {} ;

 node[Bullet,label=left :{$e_5$}] (E5) at (0,0) {} ;

 draw[thick] (E1)--(E2)--(E3)--(E4)--(E5)--(E1) {} ;

end{scope}

 begin{scope}[local bounding box=right,xshift=4cm]

 node[Bullet,label=left :{$c_1$}] (C1) at (0,2) {} ;

 node[Bullet,label=above:{$c_2$}] (C2) at (1,3) {} ;

 node[Bullet,label=right:{$c_3$}] (C3) at (2,2) {} ;

 node[Bullet,label=right:{$c_4$}] (C4) at (2,0) {} ;

 node[Bullet,label=left :{$c_5$}] (C5) at (0,0) {} ;

 draw[thick] (C1)--(C3)--(C5)--(C2)--(C4)--(C1) {} ;

end{scope}

end{scope}

path let p1=($(top.east)-(top.west)$) in

node[below=of top,align=center,text width=x1]{

rule[0cm]{x1}{0.5pt}

degree sequence

begin{alignat*}{2}

 e&={2,2,2,2,2}& c&={2,2,2,2,2}\

 delta(e)&=2 &delta(c)&=2\

 Delta(e)&=2&Delta(c)&=2

end{alignat*}

rule[0cm]{x1}{0.5pt}

begin{alignat*}{2}

 alpha(e_{1})&=c_{1},quad&alpha(e_{2})&=c_{3},\

 alpha(e_{3})&=c_{5},&alpha(e_{4})&=c_{2},\

 alpha(e_{5})&=c_{4},&alpha(e_{1})&=c_{1},

end{alignat*}

rule[0cm]{x1}{0.5pt}

begin{align*}

e_{1}&to{}e_{2}to{} e_{3}to{}e_{4}to{}

            e_{5}to{}e_{1}\

            c_{1}&to{}c_{3}to{} c_{5}to{}c_{2}to{}

            c_{4}to{}c_{1}

end{align*}

rule[0cm]{x1}{0.5pt}};

end{tikzpicture}

end{document}

with use of array:

documentclass[margin=2mm]{standalone}

usepackage{amsmath,animate}

usepackage{graphicx}

usepackage{booktabs}

usepackage{tikz}



begin{document}

$

begin{array}{@{}c @{}}

begin{array}{cc}

tikznode[draw]{includegraphics[width=31mm]{example-image-duck}};

                    & tikznode[draw]{includegraphics[width=31mm]{example-image-duck}};\

   midrule

multicolumn{2}{c}{$degree sequence$}               \[1ex]

e ={2,2,2,2,2}    & c ={2,2,2,2,2}              \

delta(e)=2         & delta(c)=2                   \

Delta(e)=2         & Delta(c)=2                   \

        end{array}                                 \    

    midrule

alpha(e_{1})=c_{1},quad   alpha(e_{2})=c_{3},    \

alpha(e_{3})=c_{5},quad   alpha(e_{4})=c_{2},    \

alpha(e_{5})=c_{4},quad   alpha(e_{1})=c_{1},    \

    midrule

e_{1}to e_{2}to e_{3}to e_{4}to e_{5}to e_{1}  \

c_{1}to c_{3}to c_{5}to c_{2}to c_{4}to c_{1}  \

    midrule

end{array}

$

end{document}

instead your tikzpicture code i use example image.